Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence

Uenishi, Hirohide; Morozumi, Takeya; Toki, Daisuke; Eguchi-Ogawa, Tomoko; Rund, Lauretta A; Schook, Lawrence B

doi:10.1186/1471-2164-13-581

Table 1 Pig cDNA libraries, ESTs, and completely sequenced cDNA clones

From: Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence

Library name	Method of library construction	Tissue/cell	Origin^a	Vector	ESTs			Sequenced cDNA
Library name	Method of library construction	Tissue/cell	Origin^a	Vector	In contigs	In singlets	Total	Clones	Mapped on Sscrofa10.2	Loci
ADR01	Oligo-capping	Adrenal gland	LWD (LWD2)	pCMVFL3	6490	3188	9678	901	861	782
AMP01	SMART	Alveolar macrophage	LWD (LWD7)	pDNR-LIB	5459	3704	9163	1416	1345	930
BFLT1	Oligo-capping	Brain (frontal lobe)	Duroc (2-14C)	pME18S	8104	5678	13,782	991	953	859
BKFL1	SMART	Backfat	Landrace (L2)	pDNR-LIB	1557	7920	9477	453	418	404
BMWN1	Vector-capping	Bone marrow	NIBS miniature	pGCAP10	5981	2492	8473	148	133	124
CBLT1	Vector-capping	Cerebellum	Duroc (2-14C)	pGCAP10	6082	3054	9136	0	0	0
CLNT1	Oligo-capping	Colon	Duroc (2-14C)	pME18S	6580	6782	13,362	537	512	365
DCI01	SMART	Immature dendritic cells	Landrace (L1)	pDNR-LIB	5953	4486	10,439	887	841	748
HTMT1	Vector-capping	Hypothalamus	Duroc (2-14C)	pGCAP10	8063	5278	13,341	1663	1474	1264
ILNT1	Vector-capping	Inguinal lymph node	Duroc (2-14C)	pGCAP10	6321	2658	8979	0	0	0
ITT01	Oligo-capping	Intestine	LWD (LWD2)	pCMVFL3	7272	2475	9747	1265	1206	1037
KDN01	Oligo-capping	Kidney	LWD (LWD8)	pME18S	5873	3235	9108	748	723	663
LNG01	Oligo-capping	Lung	LWD (LWD3)	pCMVFL3	5186	3859	9045	1331	1250	1061
LVR01	Oligo-capping	Liver	LWD (LWD4)	pCMVFL3	7199	1815	9014	779	741	653
LVRM1	Oligo-capping	Liver	Meishan	pCMVFL3	13,881	5051	18,932	1844	1760	1372
MLN01	Oligo-capping	Mesenteric lymph node	LWD (LWD2)	pCMVFL3	6443	3250	9693	1176	1099	902
MLTL1	SMART	Longissimus muscle	Landrace (L2)	pDNR-LIB	3577	4892	8469	413	388	292
OVR01	Oligo-capping	Ovary	LWD (LWD1)	pCMVFL3	6537	2828	9365	1416	1356	1226
OVRM1	Oligo-capping	Ovary	Meishan	pCMVFL3	12,471	7071	19,542	3309	3149	2665
OVRT1	Oligo-capping	Ovary	Duroc (2-14C)	pME18S	9516	4340	13,856	819	790	728
PBL01	Oligo-capping	Peripheral blood lymphocytes	LWD (LWD5)	pCMVFL3	6652	3262	9914	957	908	732
PCT01	Oligo-capping	Placenta	LWD (LWD9)	pME18S	2175	1115	3290	161	150	142
PST01	Oligo-capping	Prostate	LWD (LWD10)	pME18S	6813	2329	9142	691	654	596
PTG01	Oligo-capping	Pituitary gland	LWD (LWD4)	pCMVFL3	4281	5628	9909	864	826	790
SKNB1	Oligo-capping	Skin	Berkshire	pME18S	4894	3363	8257	687	630	534
SMG01	Oligo-capping	Submaxillary gland	LWD (LWD2)	pCMVFL3	6944	2680	9624	458	430	361
SPL01	Oligo-capping	Spleen	LWD (LWD1)	pCMVFL3	6793	2811	9604	1457	1397	1207
SPLT1	Vector-capping	Spleen	Duroc (2-14C)	pGCAP10	6037	2734	8771	0	0	0
TCH01	Oligo-capping	Trachea	LWD (LWD3)	pCMVFL3	5151	3658	8809	1412	1345	1087
TES01	Oligo-capping	Testis	LWD (LWD6)	pME18S	7112	2962	10,074	697	669	466
THY01	Oligo-capping	Thymus	LWD (LWD1)	pCMVFL3	7586	3704	11,290	2158	2066	1620
UTR01	Oligo-capping	Uterus	LWD (LWD1)	pCMVFL3	6796	2626	9422	1441	1356	1180
Total					209,779	120,928	330,707	31,079	29,430	13,894	(2993)^b

Thirty-two cDNA libraries constructed with pig tissues and cell populations were used to generate expressed sequence tags (ESTs). Twenty-three libraries were constructed by using the oligo-capping method[21], and five were constructed by using the vector-capping[20] method. Four libraries were constructed by using the SMART method (Clontech, Palo Alto, CA, USA)[22]. ESTs in contigs are shown, as are those that had a ≥100-bp stretch of Phred quality value ≥20 and were not involved in contigs (“In singlets”). Numbers of cDNA clones that were completely sequenced (31,079 in total) are also shown. Completely sequenced cDNA clones derived from pigs cloned from a female subjected to genome sequencing by the International Swine Genome Sequencing Consortium are classified by library.
^a Origins are indicated as pig breeds or lines. Different animals in the same breed are designated as described in parentheses. LWD is (Landrace × Large White) × Duroc. Duroc (2-14C) designates a Duroc individual cloned from a female pig subjected to draft genome sequencing[5–7].
^b Loci repeated among clones derived from different libraries were removed.

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ISSN: 1471-2164

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