Supplemental Table 1. Primers used for real-time PCR.

Target Gene / Genbank Accsession / 3'-Dist1
(bp) / Sequence
5'  3' / Length (nt) / Pos3 / Amplicon Length (bp)
Gapd
(3'-UTR) / NM_001001303 / 164 / caccccagcaaggacactg
ccctaggcccctcctgttatt / 19
21 / 1077
1191 / 115
Gapd / NM_001001303 / 795 / gtgatgggtgtgaaccacgag
ccacaatgccaaagttgtca / 21
20 / 446
566 / 121
Pbgd / NM_013551 / 1408 / atgtccggtaacggcggc
cgtacaaggctttcagcatcgc / 18
22 / 147
285 / 139
Actb / NM_007393 / 130 / tttttgtccccccaacttga
tcagtgtacaggccagccct / 20
20 / 1762
1833 / 91
800 / Atcattgctcctcctgagcg
tgctgatccacatctgctgg / 20
20 / 1065
1136 / 91
1600 / ggactcctatgtgggtgacga
ctgcccacttggtaacaatgc / 21
21 / 230
301 / 92
Plg / NM_008877 / 320 / GCCTGGTGTCTACGTTCGTGT
AGCAGAGGTTTTGCTCGGC / 21
19 / 2433
2511 / 97
760 / TATCCGTGGGTCGGATGTTC
GGGCGGCTTAGTTTCAGCA / 20
19 / 1995
2069 / 93
1500 / CGTCCACTACCATCACAGGGA
GCCAGCATCTGGGAAGTTCTC / 21
21 / 1226
1300 / 95
Cp / NM_007752 / 130 / TGCTGGGATGGCAACTACCT
TCGTTTTCCACTTATCGCCAA / 20
21 / 3234
3305 / 92
940 / CAAGAAGGTTGTGTATCGCCAGT
AAGGATGCCCAAGTGCTCG / 23
19 / 2427
2499 / 91
1600 / GGGCCAATGAAAATATGCAAG
CAAACACTGTGGGAAACAAGTAGAA / 21
25 / 1753
1822 / 94
Pygl / NM_133198 / 300 / GGGAAGTTCTCCAGTGACCG
GCTGGACTCGTTGGATAGGG / 20
20 / 2462
2541 / 99
900 / GCTGCCCCAGGATATCACAT
CAACTTGCTGCCGACCATG / 20
19 / 1862
1939 / 96
1700 / ACACATCCTGCACTCGCCA
TCTTCGTGATCTCCCATGCC / 19
20 / 1055
1126 / 91

1 Distance of the amplified Sequence to the poly-A-tail of the mRNA.

2 Number of the exon in which the primer sequence is located.

3 Position of the 5' nucleotide of the primer relative to the Genbank sequence.

Supplemental Table 2. Ct values and amplification factors.

T7-IVT / SMART
1 round / 2 rounds / 12 cycles / 24 cycles
close / Ct / mean±sd / 8.2 ± 0.47 / 14.5 ± 0.58 / 10.9 ± 0.43 / 17.4 ± 0.23
90%-CI1 / 7.6…8.7 / 13.8…15.1 / 10.4…11.4 / 17.1…17.6
factor2 / mean / 0.23 / 15.50 / 1.40 / 108
90%-CI / 0.16..0.33 / 0.99…24 / 1.0…2.0 / 89.6…129
medium / Ct / mean±sd / 7.4 ± 1.16 / 11.2 ± 3.09 / 10.6 ± 0.81 / 17.5 ± 1.79
90%-CI / 6…8.7 / 7.6…14.8 / 9.6…11.5 / 15.4…19.6
factor / mean / 0.14 / 1.77 / 1.15 / 119
90%-CI / 0.05…0.34 / 0.16…20 / 0.61…2.19 / 29.3…485
distant / Ct / mean±sd / 4 ± 0.99 / 6.1 ± 2.41 / 10 ± 1.72 / 15.9 ± 2.93
90%-CI / 2.8…5.1 / 3.2…8.9 / 7.9…12 / 12.4…19.3
factor / mean / 0.01 / 0.06 / 0.78 / 39.90
90%-CI / 0.006…0.031 / 0.009…0.38 / 0.20…3.03 / 3.99…398
p-value3 / medium/close / 0.1244 / 0.0421 / 0.2584 / 0.4361
distant/close / 0.0001 / 0.0003 / 0.1744 / 0.1750

1confidence intervals, calculated on the t-distribution with 3 degrees of freedom

2factors in thousands, calculated by 1.95Ct

3two sided t-test on Ct values (d.f.=7)

Supplemental Table 3. Libraries pooled for Digital Differential Display (library index and description).

Liver / Kidney
IndexDescription / IndexDescription
598Soares mouse NML
1299Sugano mouse liver mlia
1778Mus musculus adult C57BL/6J liver
1883Mus musculus liver C57BL/6J 13-day embryo
2484mouse liver, vehicle control
2525RIKEN full-length enriched, 14 days embryo liver
4141RIKEN full-length enriched, 13 days embryo liver
9742RIKEN full-length enriched, adult male liver
11113AFT024-subtracted library / 482Stratagene mouse kidney (#937315)
539Barstead MPLRB1
592GuayWoodford Beier mouse kidney day 0
596GuayWoodford Beier mouse kidney day 7
1300Sugano mouse kidney mkia
1764Mus musculus C57BL/6J kidney
5492RIKEN full-length enriched, 0 day neonate kidney
7215RIKEN full-length enriched, adult male kidney
8621NIA Mouse Newborn Kidney cDNA Library2 (Short)
9937RIKEN full-length enriched, kidney CCL-142 RAG
9979NIA Mouse Newborn Kidney cDNA Library (Long)
12249RIKEN full-length enriched, 16 days embryo kidney
12250RIKEN full-length enriched, 17 days embryo kidney
14141NIA Mouse Newborn Kidney cDNA Library (Long 1)

Supplemental Table 4. Ct values and amplification factors for Gapd and Pbgd.

T7-IVT / SMART
1 rounds / 12 cycles / 24 cycles
close / Ct / mean±sd / 9.8 ± 0.9 / 10.5 ± 2.3 / 16.2 ± 3.2
Gapd
3'UTR / 90%-CI1 / 7.6…12 / 7.9…13 / 13…19
factor2 / mean / 0.87 / 1.50 / 75.00
90%-CI / 0.2…3.9 / 0.23…9.5 / 9…625
medium / Ct / mean±sd / 7 ± 0.4 / 6.8 ± 0.8 / 13 ± 1.4
Gapd
/ 90%-CI / 6.1…7.9 / 5.8…7.8 / 12…14
factor / mean / 0.13 / 0.12 / 8.50
90%-CI / 0.07…0.25 / 0.06…0.23 / 3.3…22
distant / Ct / mean±sd / 2.8 ± 0.7 / 11.8 ± 1.8 / 17.6 ± 1
Pbgd
/ 90%-CI / 1…4.6 / 8.8…15 / 16…19
factor / mean / 7.00 / 3.50 / 200.00
90%-CI / 2…24 / 0.46…28 / 65…650

1confidence intervals, calculated on the t-distribution with 3 degrees of freedom

2factors in thousands, calculated by 1.95Ct

Supplemental Table 5. Genes present in the top-200 lists of all three assays (R: reference, T: T7-IVT, and S: SMART).

A / M / t-statistic / p value x 106 / B-statistic
(log odds ratio)
Accession / Symbol / Description / R / S / T / R / S / T / R / S / T / R / S / T / R / S / T
NM_007482 / arg1 / arginase 1 / 10.4 / 10.1 / 11.0 / 6.8 / 2.4 / 2.0 / 31605 / 7513 / 4170 / 0.08 / 0.78 / 1.16 / 8.7 / 6.6 / 5.9
NM_007469 / apoc1 / apolipoprotein ci / 11.0 / 9.6 / 10.9 / 7.9 / 3.6 / 3.6 / 30421 / 3234 / 204478 / 0.08 / 2.05 / 0.00 / 8.7 / 5.6 / 12.6
NM_007576 / c4bp / complement component 4 binding protein / 9.5 / 8.8 / 6.8 / 6.9 / 2.7 / 2.0 / 13344 / 16045 / 13525 / 0.37 / 0.27 / 0.25 / 7.4 / 7.7 / 7.4
NM_010168 / f2 / coagulation factor ii / 10.8 / 10.4 / 8.6 / 5.6 / 2.6 / 1.8 / 12191 / 11934 / 4329 / 0.45 / 0.42 / 1.10 / 7.3 / 7.2 / 6.0
NM_007376 / a2m / alpha-2-macroglobulin / 11.3 / 9.3 / 11.8 / 5.5 / 1.9 / 2.7 / 11492 / 1475 / 75045 / 0.46 / 4.38 / 0.01 / 7.2 / 4.8 / 10.4
BC013343 / similar to 4-hppa dioxygenase / similar to 4-hydroxyphenylpyruvic acid dioxygenase / 10.8 / 9.8 / 7.7 / 5.1 / 3.2 / 1.3 / 9132 / 1397 / 22 / 0.68 / 4.76 / 129.91 / 6.9 / 4.8 / 1.1
NM_007752 / cp / ceruloplasmin / 10.1 / 8.6 / 8.8 / 4.8 / 3.3 / 2.0 / 8534 / 28265 / 29440 / 0.81 / 0.11 / 0.07 / 6.8 / 8.6 / 8.6
NM_008290 / hsd17b2 / hydroxysteroid 17-beta dehydrogenase 2 / 9.2 / 8.6 / 7.5 / 4.1 / 2.2 / 2.3 / 4958 / 3887 / 40557 / 1.66 / 1.68 / 0.04 / 6.1 / 5.8 / 9.2
NM_019975 / hpcl-pending / 2-hydroxyphytanoyl-coa lyase / 9.7 / 8.1 / 9.2 / 3.7 / 1.9 / 2.9 / 2143 / 1144 / 60862 / 4.19 / 5.47 / 0.02 / 5.2 / 4.6 / 9.9
BC027200 / polypeptide b17 / similar to udp glycosyltransferase 2 family / 9.0 / 9.5 / 8.5 / 7.5 / 3.1 / 2.8 / 980 / 24115 / 49747 / 8.61 / 0.14 / 0.03 / 4.5 / 8.3 / 9.6
NM_029901 / 9430025f20rik / riken cdna 9430025f20 / 9.3 / 9.8 / 6.1 / -6.6 / -2.7 / -1.6 / -864 / -1091 / -49 / 9.44 / 5.69 / 43.87 / 4.4 / 4.6 / 2.3
NM_133198 / pygl / liver glycogen phosphorylase / 10.0 / 9.4 / 9.5 / 3.6 / 2.4 / 1.3 / 843 / 6440 / 24 / 9.63 / 0.94 / 104.21 / 4.4 / 6.4 / 1.4
NM_011804 / creg / cellular repressor of e1a-stimulated genes / 10.5 / 9.5 / 8.2 / 2.5 / 1.7 / 2.2 / 59 / 405 / 41345 / 59.98 / 12.17 / 0.04 / 2.4 / 3.8 / 9.2
NM_008087 / gas2 / growth arrest specific 2 / 9.2 / 6.8 / 5.3 / -2.4 / -1.9 / -0.9 / -30 / -641 / -12 / 108.38 / 9.08 / 654.65 / 1.8 / 4.1 / -0.5
NM_025655 / 2010002a20rik / riken cdna 2010002a20 / 8.0 / 8.8 / 6.5 / -5.0 / -2.2 / -1.0 / -22 / -1658 / -23 / 222.72 / 3.94 / 124.19 / 1.1 / 5.0 / 1.2
NM_012033 / tinag / tubulointerstitial nephritis antigen / 7.2 / 8.7 / 9.1 / -3.5 / -2.0 / -1.1 / -22 / -1290 / -44 / 220.90 / 4.93 / 45.23 / 1.0 / 4.7 / 2.2
BC020021 / 2810439f02rik / riken cdna 2810439f02 gene / 9.4 / 8.3 / 8.0 / 2.1 / 1.9 / 1.7 / 18 / 1072 / 4082 / 391.20 / 5.77 / 1.18 / 0.4 / 4.6 / 5.9