Summary of Data on cDNA Libraries
| Library ID | Developmental stage/tissue | Pormalizing driver (Rot) | Subtracting driver (RoT) | Method | Titer | Insert size (kbp) | Sequencing | Speies | Redundancy | No. ESTs (%) | No. NT (%) | Unique (%) | Coding (%) | |||
| 18–100 | Adult/pancrea | mRNA (5) | ms1 (20) | 1 | 8.20e + 04 | 1.2 | 13556 | 3402 | 3.98 | 307 | (9.0) | 873 | (25.7) | 442 | (13.0) | (100.0) |
| 22–000 | Adult/stomach | (standard) | (standard) | 5.90e + 04 | 0.88 | 1458 | 488 | 2.99 | 26 | (5.3) | 52 | (10.7) | 42 | (8.6) | (82.1) | |
| 22–100 | mRNA (5) | ms1 (20) | 1 | 3.50e + 05 | 1.21 | 4400 | 1932 | 2.28 | 120 | (6.2) | 324 | (16.8) | 196 | (10.1) | (82.1) | |
| 22–104 | mRNA (5) | ms1 (20), Nm1 (5) | 1 | 2.00e + 05 | 1.13 | 3936 | 1862 | 2.11 | 144 | (7.7) | 302 | (16.2) | 207 | (11.1) | (82.1) | |
| 23–000 | Adult/tongue | (standard) | (standard) | 4.10e + 04 | 1179 | 556 | 2.12 | 30 | (5.4) | 50 | (9.0) | 36 | (6.5) | 76.8 | ||
| 23–100 | mRNA (5) | ms1 (20), Nm1 (5) | 1 | 4.10e + 04 | 1.44 | 10267 | 4017 | 2.56 | 410 | (10.2) | 992 | (24.7) | 586 | (14.6) | 76.8 | |
| 24–100 | ES cell | mRNA (5) | ms1 (20), Nm1 (5) | 1 | 1.30e + 05 | 1.77 | 15226 | 4495 | 3.39 | 236 | (5.3) | 677 | (15.1) | 485 | (10.8) | (88.6) |
| 25–100 | Embryo13/liver | mRNA (5) | ms1 (20), Nm1 (5) | 1 | 8.50e + 04 | 1.19 | 5448 | 1525 | 3.57 | 52 | (3.4) | 179 | (11.7) | 168 | (11.0) | (92.2) |
| 26–000 | Embry10/whole boy | (standard) | (standard) | 6.10e + 05 | 1.38 | 2108 | 1061 | 1.99 | 31 | (2.9) | 97 | (9.1) | 71 | (6.7) | 92.3 | |
| 26–100 | mRNA (7.5) | ms1 (30), Nm1 (7.5) | 1 | 5.00e + 05 | 1.32 | 11267 | 4722 | 2.39 | 330 | (7.0) | 870 | (18.4) | 582 | (12.3) | 92.3 | |
| 28–100 | Embryo 10 + 11/whole body | mRNA (7.5) | ms1 (30), Nm1 (7.5) | 1 | 8.80e + 05 | 1.29 | 6248 | 3411 | 1.83 | 190 | (5.6) | 450 | (13.2) | 271 | (7.9) | (93.9) |
| 28–104 | mRNA (7.5) | ms1 (30), Nm1 (7.5) | 1 | 8.80e + 05 | 1.38 | 9321 | 4335 | 2.15 | 293 | (6.8) | 672 | (15.5) | 453 | (10.4) | (93.9) | |
| 31–000 | Embryo/head | (standard) | (standard) | 4.90e + 04 | 1.22 | 488 | 369 | 1.32 | 12 | (3.3) | 30 | (8.1) | 23 | (6.2) | (86.2) | |
| 31–100 | mRNA (10) | ms1 (40), Nm1 (10) | 1 | 4.20e + 05 | 1.55 | 7838 | 4229 | 1.85 | 344 | (8.1) | 682 | (16.1) | 494 | (11.7) | (86.2) | |
| 32–304 | Embryo14 + 17/head | mRNA (10) | ms1 (40), Nm1 (10) Nm2 (10) | 1 | 3.30e + 05 | 2.5 | 424 | 389 | 1.09 | 22 | (5.7) | 41 | (10.5) | 20 | (5.1) | (88.2) |
| 38–304 | Embryo11/placenta & extraembryonl c tissue | mRNA (10) | ms1 (40), Nm2 (10) | 2 | 2.60e + 06 | 1.45 | 3657 | 2165 | 1.69 | 98 | (4.5) | 255 | (11.8) | 156 | (7.2) | (100.0) |
| 39–304 | Embryo13/whole body | mRNA (10) | ms1 (40), Nm1 (10) Nm2 (10) | 2 | 2.10E + 05 | 2.47 | 348 | 319 | 1.09 | 14 | (4.4) | 33 | (10.3) | 22 | (6.9) | (90.0) |
| 49–304 | Adult/testis | mRNA (10) | ms2 (90), Nm2 (10) | 2 | 2.60E + 06 | 2.11 | 8900 | 5444 | 1.63 | 1102 | (20.2) | 1443 | (26.5) | 1214 | (22.3) | (95.7) |
| 52–304 | Adult/Xiphoid | total RNA (3) | ms2 (90), Nm2 (10) | 2 | 7.30e + 05 | 2.69 | 272 | 256 | 1.06 | 12 | (4.7) | 21 | (8.2) | 15 | (5.9) | (100.0) |
| 53–304 | Adult/pituitary grand | total RNA (3) | ms2 (90), Nm2 (10) | 2 | 2.10e + 06 | 2.38 | 8059 | 4658 | 1.73 | 411 | (8.8) | 640 | (13.7) | 833 | (17.9) | (100.0) |
| 54–304 | Neonate6/head | mRNA (10) | ms2 (90), Nm2 (10) | 2 | 1.30e + 06 | 2.3 | 2663 | 2101 | 1.27 | 115 | (5.5) | 217 | (10.3) | 196 | (9.3) | (90.0) |
| 55–304 | Neonate10/head | mRNA (10) | ms2 (90), Nm2 (10) | 2 | 1.70e + 06 | 2.18 | 603 | 525 | 1.15 | 39 | (7.4) | 83 | (15.8) | 44 | (8.4) | 77.3 |
| 56–304 | Embryo6/whole body | (subtracted only) | ms2 (90), Nm2 (10) | 2 | 6.00e + 05 | 2.3 | 416 | 371 | 1.12 | 10 | (2.7) | 25 | (6.7) | 16 | (4.3) | (100.0) |
| 57–304 | Embryo8/whole body | (subtracted only) | ms2 (90), Nm2 (10) | 2 | 1.20e + 06 | 1.91 | 19632 | 7758 | 2.53 | 778 | (10.0) | 1598 | (20.6) | 1155 | (14.9) | (100.0) |
| 58–304 | Adult/thymus | mRNA (10) | ms2 (90), Nm2 (10) | 2 | 1.70e + 06 | 3.27 | 10259 | 6442 | 1.59 | 604 | (9.4) | 1074 | (16.7) | 1100 | (17.1) | (80.0) |
| 60–304 | Embryo13/testis | total RNA (5) | ms2 (90), Nm2 (10) | 2 | 5.70e + 05 | 11079 | 6498 | 1.7 | 672 | (10.3) | 1122 | (17.3) | 1243 | (19.1) | (75.0) | |
| 61–304 | Embryo14/thymus | (subtracted only) | ms2 (90), Nm2 (10) | 2 | 4.80e + 05 | 4.13 | 206 | 196 | 1.05 | 9 | (4.6) | 24 | (12.2) | 16 | (8.2) | (60.0) |
| 62–304 | Enbryo11/head | mRNA (10) | ms2 (90), Nm2 (10) | 2 | 3.30e + 05 | 2.19 | 2967 | 2374 | 1.25 | 149 | (6.3) | 265 | (11.2) | 256 | (10.8) | (70.0) |
[i] The library ID is the identification number in the RIKEN database. The sublibrary ID is 000 for the standard library and 100, 104, or 304 for the subtracted/normalized cDNA libraries. In the subtracting or normalizing driver column, the value in brackets indicates the RoT used for each driver. The normalizing driver was always an aliquot of the starting RNA. The subtracting driver was mn1, minilibrary of liver, lung, brain, and placenta; mn2, minilibrary of liver, lung, brain, placenta, testis, pancreas, small intestine, stomach, and tongue; Nm1, RIKEN nonredundant minilibrary (4000 clones); Nm2, RIKEN nonredundant minilibrary (1600 clones). The Method column indicates the method used to label the mRNA driver. Method 1, chemical end-biotinylation (Na104-biotin hydrazide long arm for cap and 3′-end of mRNA), enzymatic biotinylation (during RNA polymerase treatment using biotin-UTP), and biotin-psoralen (all RNAs); Method 2: Label IT biotin labeling kit only. Sequencing indicates the number of 3′-end sequencing passes. Species indicates the number of different species (clusters) obtained. Redundancy is the obtained redundancy (sequence/species). No. ESTs and No. NT indicate the number and percentage of sequences from the cDNA library that do not have relevant homology with EST or GenBank nucleotides (nonredundant GenBank +EMBL +DDBJ +PDB sequences), respectively. The percentage value refers to the number of clusters (species) and not to the number of total successful sequence. Coding indicates the percentage of clones among the mouse, complete mRNA that had the initiating ATG, as evaluated by 5′-end sequencing. Values in parentheses are when clones are <50 (but at least 10).