Table 1

cDNA libraries

Lib name

Tissue (Animals)

Description

Reads


Amn

Amnion (S)

-

2,394

Aor

Aorta (M)

-

5,121

Bla

Bladder (M)

-

8,042

Nbma

Bone marrow (S)

115 days, bone marrow

10,068

Cbe

Brain (M)

Cerebellum

4,180

Cbrb

Brain (B)

Brain (cortex)

7,814

Fco

Brain (M)

Frontal cortex

6,361

Hyp

Brain (S)

Hypothalamus

7,001

Pgl

Brain (M)

Pituitary gland

8,440

Ecca

Brain (S)

F 50 days, cortex

8,693

Ecea

Brain (S)

F 50 days, cerebellum

4,361

Fcea

Brain (S)

F 100, cerebellum

3,682

Fcca

Brain (S)

F 107, cortex cerebri

5,056

Fhia

Brain (S)

F 107 Hippocampus

5,897

Cblb

Haemopoetic (B)

Blood

8,711

Jca

Cartillage (S)

Joint capsule

8,775

Ncaa

Cartillage (S)

115 days, cartilage

7,306

Panb

Endocrine glands (M)

Pancreas

4,238

Ret

Eye (M)

Retina

7,768

Eyea

Eye (S)

F 50, eye

5,865

Fat

Fat (M)

Fat

6,783

Che

Heart (B)

-

7,336

Hea

Heart (M)

-

4,890

Hlv

Heart (S)

Left ventricle

7,181

Cje

Intestine (B)

Jejunum

6,052

Col

Intestine (S)

Large intest, colon asc.

5,128

Duo

Intestine (S)

Small intest, duodenum

5,787

Ill

Intestine (S)

Small intest, illeum

5,695

Jej

Intestine (S)

Small intest, jejunum

10,109

Lin

Intestine (M)

Large intestine

6,868

Sin

Intestine (M)

Small intestine

5,716

Ejea

Intestine (S)

F 50, Jejunum

10,118

Ncoa

Intestine (S)

115 days, colon

6,183

Njea

Intestine (S)

115 days, jejunum

6,027

Cki

Kidney (B)

-

6,052

Kid

Kidney (M)

-

7,708

Cli

Liver (B)

-

6,544

Liv

Liver (M)

-

6,836

Elia

Liver (S)

F 50, liver

6,587

Flia

Liver (S)

F 100, liver

4,929

Clu

Lung (B)

-

8,358

Lunc

Lung (M)

-

6,645

Elua

Lung (S)

F 50 days, lung

2,595

Nlua

Lung (S)

115 days, lung

5,217

Cly

Lymphatic gland (B)

-

8,289

Lyg

Lymphatic gland (M)

-

7,513

Lnt

Lymphatic gland (S)

-

7,027

Cga

Mammary gland (B)

-

3,583

Mcp

Mammary gland (S)

Mammae, collostrum prod

5,860

Mga

Mammary gland (M)

7 days after weaning

6,242

Mgmb

Mammary gland (M)

14 days after birth

5,545

Mgp

Mammary gland (M)

7 days pre-birth

4,335

Med

Mediastinum (S)

-

8,602

Bfe

Muscles (M)

M. biceps femoris

6,673

Ctlb

Muscles (B)

Tenderloin

6,533

Isp

Muscles (M)

M. infraspinatus

6,650

Ldo

Muscles (M)

M. longissimus dorsi

10,309

Mas

Muscles (S)

M. masseter

4,755

Sme

Muscles (M)

M. semimembranosus

3,274

Ssp

Muscles (M)

M. supraspinatus

7,379

Ste

Muscles (M)

M. semitendinosus

7,396

Tbr

Muscles (M)

M. triceps brachii

6,486

Vin

Muscles (M)

M. vastus intermedius

3,007

Esea

Muscles (S)

F 50, M. semitendinosus

7,905

Nmsa

Muscles (S)

115 days, M. semitendinosus

4,676

Gul

Oesophagus (M)

-

5,631

Ova

Ovary (M)

-

7,744

Cov

Ovary (S)

-

7,567

Plad

Placenta (M)

-

7,481

Pro

Prostata (M)

-

1,953

Rec

Rectum (M)

-

5,778

Cmu

Rhinal mucosal membrane (B)

-

5,365

Nmma

Rhinal mucosal membrane (S)

115 days, mucosal memb.

7,530

Sag

Salivary gland (M)

-

5,473

Csk

Skin (B)

-

7,105

Ski

Skin (M)

-

6,815

Ton

Skin (S)

Tip of tongue, mucosa

5,698

Eepa

Skin (S)

F 50, epidermis

8,159

Erua

Skin (S)

F 50, regium bilicalis

8,330

Nepa

Skin (S)

115 days, epidermis

5,437

Spc

Spinal cord (M)

Spinal cord

8,821

Ebsa

Spinal cord (S)

F 50 days, brainstem

8,453

Fbsa

Spinal cord (S)

F 107 brainstem

5,703

Spl

Spleen (M)

-

6,984

Csp

Spleen (B)

-

6,204

Cst

Stomach (B)

-

7,141

Sto

Stomach (M)

-

5,561

Sug

Suprarenal glands (M)

-

7,856

Cag

Suprarenal glands (B)

Adrenal gland

6,614

Cte

Testicle (B)

-

3,416

Tes

Testicle (M)

-

4,812

Cty

Thyroid glands (B)

-

9,608

Thg

Thyroid glands (M)

-

7,887

Pty

Thyroid glands (S)

Piglet 2 days, thymus

7,007

Ftya

Thyroid glands (S)

F 100, thymus

5,687

Tra

Trachea (M)

-

8,124

Ute

Uterus (S)

-

7,531

Cut

Uterus (B)

-

5,885


The generated cDNA libraries, representing 35 tissues. They are here shown as two (overlapping) sets: a physiologic set and a developmental set. The column 'Lib name' gives three letter code for the library. 'Tissue' indicates the overall tissue the library was generated from, where '(Animals)' indicates whether the library was generated from a single (S or B) or multiple (M) animals. Libraries listed with (M) and (S) represent the pig breeds (mostly cross-breeds) used in Danish breeding (Landrace, Yorkshire, Duroc, and Hampshire), whereas the libraries listed with (B) present Chinese pig breeds. 'Description' provides a short description. The column 'Reads' shows the number of reads that went into that library after cleaning. The sum of all 'Reads' corresponds to the number of generated reads that contributed to the assembly, that is the number of reads after cleaning vector, repeats, and so on. Library names beginning with 'C' originates from Chinese pig breeds (except for 'Col' and 'Cbe'), whereas the remaining libraries originated from Danish pig breeds. aDevelopmental tissue. bIgnored in expression analysis (see Materials and methods). cLikely to be heavily contaminated by liver expressed sequence tags. dA normalized library.

Gorodkin et al. Genome Biology 2007 8:R45   doi:10.1186/gb-2007-8-4-r45

Open Data