Table 1.

cDNA Libraries and Their Sequencing

Library ID	Develop. stage	Strain	Organ/tissue (E) embryo, L) Lactation, (Po) Postnatal (Pr) Pregnancy	Age (E) embryo, (L) Lactation, (Po) Postnatal (Pr) Pregnancy	Other conditions	Vector: λ if not specified	Insert size	Size sel.	RNA notes	Normalization and sub. status	Normarization drivers (RoT)	Norm. RoT (CoT)	Sub. drivers (RoT)	Sub. RoT (CoT)	Library ID	Total RoT (CoT)	Yield = % that was not sub.	Sublib ID	3′ seq. clones	3′ clusters + singl.	3′ red.	3′ cluster without hit to known genes	3′ unique clusters + singl.	Pres. of poly A signals	3′ complete CDS	5′ seq. clones	5′ clusters + singl.	5′ red.	5′ cluster without hit to known genes	5′ unique clusters + singl.	5′ complete CDS
01	stage1	C57BL/6J	blastocyst			TripIEx	N.A.		total	Std					01		Std	01-000	156	154	1.01	10	21	100	(82.00)	954	869	1.10	49	290	75.05
						Zap	1.27 K			Std							Std	06-000	—	—	—	—	—	—	—	256	179	1.43	7	27	95.93
06	stage28	C57BL/6J	kidney												06
						Zap	1.40 K			Nor	mRNA (5)	5					N.A.	06-100	4491	1422	3.16	43	97	3867	99.31	1292	1013	1.28	23	171	92.72
						Zap	1.09 K			Std							Std	07-000	—	—	—	—	—	—	—	78	71	1.10	3	13	(91.67)
07	stage28	C57BL/6J	brain												07
						Zap	1.02 K			Nor	mRNA (5)	5					N.A.	07-100	461	294	1.57	3	22	374	99.00	67	66	1.02	2	19	(84.85)
08	stage28	C57BL/6J	lung			Zap	0.80 K			Nor					08		N.A.	08-100	—	—	—	—	—	—	—	77	52	1.48	12	19	(97.78)
09	stage28	C57BL/6J	spleen			Zap	0.80 K			Nor					09		N.A.	09-100	366	128	2.86	3	9	344	99.64	384	108	3.56	5	25	96.70
						Zap	0.99 K			Std							Std	10-000	—	—	—	—	—	—	—	115	67	1.72	4	8	94.34
10	stage28	C57BL/6J	heart			Zap	0.76 K			Nor					10		N.A.	10-100	271	160	1.69	2	3	245	97.60	260	158	1.65	3	31	93.10
						FLCI	1.80 K			Std							Std	10-200	666	447	1.49	24	26	551	98.53	553	395	1.40	26	75	91.82
						Zap	0.75 K			Std							Std	11-000	243	179	1.36	5	5	209	99.32	303	230	1.32	13	88	79.58
11	stage26	C57BL/6J	E 18 whole body			Zap	0.97 K			Nor					11		N.A.	11-100	10887	4057	2.68	189	277	9458	99.20	1565	1504	1.04	46	811	62.01
						Zap	0.99 K			Nor							N.A.	11-900	6665	1978	3.37	78	70	5799	99.29	185	182	1.02	15	102	57.75
						Zap	2.36 K			Std							Std	12-000	2343	1204	1.95	104	52	1972	99.80	588	547	1.07	32	132	89.30
12	stage28	C57BL/6J	lung												12
						Zap	1.31 K			Nor							N.A.	12-100	161	148	1.09	4	2	132	99.03	298	269	1.11	9	68	92.05
13	stage28	C57BL/6J	liver			Zap	2.42 K			Std					13		Std	13-000	1665	807	2.06	34	47	1461	99.77	343	329	1.04	7	52	92.35
						FLCI	3.73 K	Yes		Std							Std	14-210	40	32	1.25	4	1	31	(100.00)	28	24	1.17	7	7	(100.00)
14	stage28	C57BL/6J	brain			FLCI	2.53 K	Yes		Std					14		Std	14-220	40	36	1.11	2	2	34	(100.00)	22	20	1.10	2	6	(100.00)
						FLCI	3.61 K	Yes		Nor							N.A.	14-320	35	18	1.94	2	1	33	(100.00)	29	15	1.93	1	3	(100.00)

Summary of libraries, clones, and sequencing resources. Libraries are listed by ID order. (Sub-libraries ID) Different cloning events form the same mRNA/first-strand cNDA reaction. See Methods for details on subtraction drivers. (Unique) Number of cDNAs that derive from a given library only. (Poly(A) signal) The presence of the top 6 signal as in Table 5. (Subtraction and normalization) Subtraction is with RNA (RoT) unless specified (CoT), which corresponds to DNA. (N.A.) Not available; (Std) standard; (Sub.) subtraction; (Nor) normalization; (Seq.) sequenced; (Singl.) singletons; (red.) redundancy; (pres.) presence; (Size sel.) size selection; (ssDNA) single strand DNA; (Total RNA) no poly(A) selection