Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

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

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  1. Genome Res. 13: 1273-1289

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