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Radiosonde Daytime Biases and Late–20th Century Warming

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         realizations reduces noise and facilitates signal            temperatures of 28.0- and 28.2-C and 80% relative              Climate Variability and Predictability Working Group on
         estimation.                                                  humidity. These are conditions typical of deep                 Coupled Modeling and their Coupled Model Inter-
   25.   Materials and methods are available as supporting            convective regions over the tropical oceans. The               comparison Project and Climate Simulation Panel for
         material on Science Online.                                  pseudo-adiabats correspond to equivalent potential             organizing the model data analysis activity, and the IPCC
   26.   F. J. Wentz, M. Schabel, Nature 403, 414 (2000).             temperatures of 353.2 and 354.1 K. The assumed                 WG1 TSU for technical support. The IPCC Data Archive
   27.   T. M. Smith, R. W. Reynolds, J. Clim.18, 2021 (2005).        temperature difference of 0.2-C corresponds approx-            at LLNL is supported by the Office of Science, U.S. DOE.
   28.   P. D. Jones, A. Moberg, J. Clim. 16, 206 (2003).             imately to the total change in tropical ocean tem-             The static MSU weighting functions and UAH MSU data
   29.   HadCRUT2v is the designation for version 2 of the            perature over the years 1979 to 1999. Theoretical              were provided by J. Christy (UAH). We thank I. Held, T.
         (variance-corrected) Hadley Centre/Climatic Re-              scaling ratios are relatively insensitive to reasonable        Delworth (both Geophysical Fluid Dynamics Laboratory),
         search Unit surface temperature data set.                    variations in the baseline values of surface air tem-          D. Easterling (National Climatic Data Center), B. Hicks
   30.   Q. Fu, C. M. Johanson, S. G. Warren, D. J. Seidel,           perature and relative humidity, as well as to the              (NOAA Air Resources Laboratory), and two anonymous
         Nature 429, 55 (2004).                                       magnitude of the surface air temperature increase.             reviewers for useful comments. O. Boucher (Hadley
   31.   P. H. Stone, J. H. Carlson, J. Atmos. Sci. 36, 415       35. V. Ramaswamy et al., in Climate Change 2001: The               Centre), G. Flato (Canadian Climate Centre), and E.
         (1979).                                                      Scientific Basis, J. T. Houghton et al., Eds. (Cambridge       Roeckner (Max-Planck Institute for Meteorology) sup-
   32.   Here, we define X as the arithmetic mean of the              Univ. Press, Cambridge, 2001), pp. 349–416.                    plied information on the historical forcings used by
                                      1
                                        P
                                        N
                                                                  36. B. D. Santer et al., Science 301, 479 (2003).                  CNRM-CM3, CCCma-CGCM3.1(T47), and ECHAM5/
         ensemble means, i.e., X 0 N       X j , where N is the
                                       j01                        37. Work at Lawrence Livermore National Laboratory                 MPI-OM.
       total number of models in the IPCC archive and X j is          (LLNL) was performed under the auspices of the U.S.
       the ensemble mean signal of the jth model. This                Department of Energy (DOE), Environmental Sci-             Supporting Online Material
       weighting avoids undue emphasis on results from a              ences Division, contract W-7405-ENG-48. A portion          www.sciencemag.org/cgi/content/full/1114867/DC1
       single model with a large number of realizations.              of this study was supported by the U.S. DOE, Office        Materials and Methods
   33. One measure of ENSO variability is s(TNINOj3.4), the
                                                   ˜                  of Biological and Environmental Research, as part of       Fig. S1
       standard deviation of sea-surface temperatures in the          its Climate Change Prediction Program. T.M.L.W. was        Table S1
          ˜
       Nino 3.4 region of the equatorial Pacific. Values of           supported by NOAA Office of Climate Programs (Cli-         References and Notes
       s(TS) in the 49 IPCC realizations are closely correlated       mate Change Data and Detection) grant NA87GP0105.
       with s(TNINOj3.4) (correlation coefficient r 0 0.92).
                  ˜                                                   P.W.T. and G.J. were funded by the UK Department of        16 May 2005; accepted 27 July 2005
   34. The theoretical expectation plotted in Fig. 3 was              the Environment, Food, and Rural Affairs. We acknowl-      Published online 11 August 2005;
       computed by taking the difference of two pseudo-               edge the international modeling groups for providing       10.1126/science.1114867
       adiabats calculated from surface air parcels with              their data for analysis, the Joint Scientific Committee/   Include this information when citing this paper.



                                                                                                                                 not clear how successful the above efforts
                Radiosonde Daytime Biases and                                                                                    may have been in detecting discontinuities—
                                                                                                                                 or avoiding false adjustments—of amplitudes
                 Late–20th Century Warming                                                                                       well below 1-C.
                                                                                                                                     Here we adopt a strategy for quantifying
                 Steven C. Sherwood,1* John R. Lanzante,2 Cathryn L. Meyer1                                                      trend errors that does not require identifying
                                                                                                                                 specific change events. The strategy applies
             The temperature difference between adjacent 0000 and 1200 UTC weather                                               only to the solar heating error and does not
             balloon (radiosonde) reports shows a pervasive tendency toward cooler daytime                                       detect other errors. It relies on the fact that the
             compared to nighttime observations since the 1970s, especially at tropical                                          diurnal temperature range in the free tropo-
             stations. Several characteristics of this trend indicate that it is an artifact of                                  sphere, hence its expected trend, is small and
             systematic reductions over time in the uncorrected error due to daytime solar                                       has known characteristics that differ from those
             heating of the instrument and should be absent from accurate climate records.                                       expected from a radiation error.
             Although other problems may exist, this effect alone is of sufficient magnitude to                                      The diurnal temperature variation in Earth_s
             reconcile radiosonde tropospheric temperature trends and surface trends during                                      atmosphere is a tide arising from its direct solar
             the late 20th century.                                                                                              heating and from diurnal variations of con-
                                                                                                                                 vective heating driven by the diurnal variation
   Atmospheric models and simple thermody-                            Among the most serious known problems is                   of surface temperature. Atmospheric heating,
   namic arguments indicate that tropospheric                     bias due to solar heating of the temperature                   which occurs primarily in the stratosphere via
   and surface temperature changes should be                      sensor (10). For many radiosonde designs this                  ozone absorption, drives migrating resonant
   closely linked (1). Radiosonde data during the                 can elevate the temperature several -C above                   oscillations that cause temperature fluctuations
   late 20th century, however (2–5), have not                     ambient during daylight, an effect that must                   of several -C in the upper stratosphere. In the
   shown warming commensurate with that re-                       be removed via an estimated correction. For                    troposphere, weaker solar heating occurs due
   ported for the surface (1, 6, 7). The main dis-                other designs no correction is standard even                   mainly to near-infrared absorption by water
   crepancy is in the Tropics during the last two                 though the effect may not be completely ab-                    with a contribution from dark aerosols. These
   decades of the 20th century.                                   sent. Adjustment of climate records for in-                    influences produce diurnal temperature fluctu-
       A number of design changes to radiosonde                   strument changes using their documented                        ations of 1-C or less in the free troposphere
   systems over the years may have affected                       histories is problematic (8, 11).                              (17). Near the land surface, variations of 5- to
   trends (8). Indeed, the spread of trends among                     One can try to remove undocumented arti-                   15-C occur due to surface diurnal heating
   stations well exceeds that implied by satellite                facts by careful examination of the data itself.               (18); over oceans, variations are È1-C.
   data (9), suggesting that trends in the obser-                 Several such efforts have detected hundreds or                     Because atmospheric tides are a linear
   vation bias typically exceed those of the                      thousands of apparent artifacts (3–5, 12). Their               phenomenon (19), the diurnal variation of
   actual temperature at individual stations.                     net effect on trends was found to be large only                temperature is proportional to that of the
                                                                  in the stratosphere. Revised trends were still                 heating, though the two need not be in phase.
                                                                  lower than those indicated by the Microwave                    Trends of È j0.2-C per decade are evident in
   1
    Department of Geology and Geophysics, Yale Uni-               Sounding Unit (MSU) in both the troposphere                    the land surface diurnal temperature range
   versity, New Haven, CT 06520, USA. 2National Oceanic
   and Atmospheric Administration/Geophysical Fluid
                                                                  and stratosphere (13). Because empirical sepa-                 (DTR) (20), which amount to about 2% of the
   Dynamics Laboratory, Princeton University, Princeton,          ration of artificial discontinuities from genuine              mean DTR per decade. Tropospheric water
   NJ 08542, USA.                                                 variability is extremely challenging in correlated             vapor and stratospheric ozone changes do not
   *To whom correspondence should be addressed.                   time series (14, 15), especially as changes can                exceed a few percent per decade in recent
   E-mail: ssherwood@alum.mit.edu                                 probably occur in many small steps (16), it is                 decades (21, 22), and absorption increases

1556                                                  2 SEPTEMBER 2005 VOL 309                  SCIENCE        www.sciencemag.org
                                                                                                                                       REPORTS
weakly with concentration due to line satu-          radiosonde temperature data (17). Conse-           been reported previously (3, 4, 27). Trends
ration (23). It follows that tides could not         quently, we expect peak DT magnitudes near         were small in North America and most of
have changed by more than a few percent,             90-E and 90-W. However, before the 1980s           Asia. We see no evidence in Fig. 2 that the
or È 0.01- to 0.02-C per decade. Because of          DT peaked broadly around 0- and 180-, where        DT trends at stations in the LKS subset dif-
this, trends in the observed day minus night         solar heating was greatest. Only by the late       fered systematically from those at neighbor-
difference in radiosonde temperatures should         1990s did the pattern in the troposphere begin     ing, non-LKS stations. However, the most
provide a sensitive detector of changes in the       to appear as expected.                             affected stations tend to be in sparsely
daytime observation bias.                                To quantify the anomalous signal, we           sampled areas where they would be strongly
    We examine the diurnal range using the           defined an additional quantity DT¶, equal to       weighted in any spatially representative clima-
CARDS data set with no adjustments (24). We          TDT with sign determined by longitude to           tology. We omitted all Indian stations from
calculated a quantity DT equal to the temper-        make it daytime (6 am to 6 p.m.) minus night-      subsequent analysis, because these show
ature difference between adjacent 0000 UTC           time. To minimize sunrise-time ambiguities,        anomalously large DT and have other prob-
and 1200 UTC sonde flights, wherever such            we did not compute DT¶ at stations within 10-      lems (3, 4).
pairs were available. Pairs were used regard-        of the 90-E/W meridians.                               Following LKS, we averaged DT¶ over
less of which time of day came first, but DT             A map of the trend in upper tropospheric       three belts: the Tropics, the Northern Hemi-
was always defined as temperature at 0000            DT¶ (Fig. 2) reveals regional variations. The      sphere extratropics (NH), and the Southern
minus temperature at 1200. At all CARDS              largest trends occurred in the Tropics, par-       Hemisphere extratropics (SH). Because tropo-
stations with sufficient data, we fitted linear      ticularly among Indian, African, and island        spheric temperature is expected to lag insola-
trends to DT for the same periods (1959 to           stations where transitional problems have          tion by about 6 hours, the zonal means bDT¶À
1997 and 1979 to 1997) documented by
Lanzante et al. (LKS) (3). LKS considered                                                                             Fig. 1. Trend in 50-hPa DT (0000
temperature trends at 87 stations denoted here                                                                        UTC T minus 1200 UTC T ) during
as the BLKS subset.[                                                                                                  1979 to 1997 versus longitude at
    Figure 1 shows the 1979 to 1997 trend in                                                                          all Tropical stations. Sine wave
stratospheric DT at tropical stations plotted                                                                         (not a curve fit) represents the
by longitude, together with a sinusoid repre-                                                                         negative of solar forcing of DT,
                                                                                                                      peaking where 0000 UTC falls at
senting the local time of day at 0000. These                                                                          midnight and troughing where it
data show that the trend is in phase with so-                                                                         falls at noon. Error bars are 1s
lar heating, with daytime readings growing                                                                            sampling uncertainties.
cooler compared to nighttime readings, and
is pervasive.
    Although clearest in the stratosphere, these
characteristics appear also at tropospheric
levels. Indeed, tropospheric and stratospheric
DT trends are highly correlated in general:
for example, r 0 0.85 between 50 and 300
hPa over 1959 to 1997. This is not true for
natural temperature variability, which tends
to be anticorrelated below and above the
tropopause in both low and high latitudes
(25), nor is it true of the tide itself. Accord-
ing to wind data, tidal fluctuations in the
troposphere should lag those at 50 hPa by
about 6 hours (26); this is also simulated by
the National Center for Atmospheric Re-
search (NCAR) Community Atmosphere Mod-
el (CAM3) (not shown) and appears (albeit
with slightly less shift) in carefully selected

Table 1. Mean difference in DT trend from 1979
to 1997, vertically weighted according to the MSU
channel 2 profile, sonde minus MSU (first two
columns) among LKS stations; the differences in
this quantity between the two station types (third
column); and prediction of the latter based on
assumptions in text (last column). All quantities
are in -C per decade. Figures in parentheses are
the number of stations used (29).

Daytime                                Predicted
              Twice daily Difference
 only                                  difference

                  Tropics
j0.228 (17) j0.102 (8)     0.130       0.120 (18)    Fig. 2. Trends in 300-hPa day-night difference DT ¶ during 1979 to 1997, in K per decade. LKS
                Extratropics                         station subset is indicated by large squares. One station (Mumbai) is off scale (not shown). Solid
j0.052 (4) j0.029 (43)     0.023       0.050 (38)    symbols are significant at 95% confidence level; thick open symbols do not pass the test at 300
                                                     hPa but are significant in the stratosphere (50 hPa).

                                          www.sciencemag.org      SCIENCE     VOL 309     2 SEPTEMBER 2005                                                1557
   REPORTS
   should be small due to near-cancellation of                 The linear trend in bDT¶À is shown by al-           caused tropospheric DT to change by only
   different longitudes.                                   titude in Fig. 4 for the two LKS time periods,          13%.) Indeed, if a 0.5-C change in diurnal
       The time series of tropical upper tropospheric      for all three belts. It increases rapidly in the        temperature range were caused by a change in
   bDT ¶À (Fig. 3), however, shows significant             stratosphere, is weak in NH but strong in the           daytime heating from any source, then the
   long-term variations. Daytime temperatures              other two belts, and is much stronger during            radiative relaxation time scale of È1 month
   warmed before about 1971, reaching values               the 1979 to 1997 period than the longer period          for deep perturbations (28) would imply a
   near 0.5-C above nighttime temperatures, then           starting in 1959.                                       change in equilibrium temperature of 10- to
   began a slow cooling trend. By the mid- to late             This trend appears unrealistic in several           20-C. Clearly, nothing like this has happened.
   1990s, bDT¶À finally dropped to a level com-            respects. First, it is almost two orders of mag-        Moreover, the spatial patterns of this trend are
   mensurate with predictions. The trend was               nitude larger than can be justified physically          inconsistent with absorbing aerosol (which
   particularly strong during the satellite era            based on the known forcings. (A run of the              decreases with height and is scanty in SH) or
   beginning in 1979. Since 1997 the trend has             CAM3 general circulation model with half-               convective heating (absent in the stratosphere)
   leveled off.                                            normal ozone, an unrealistically large change,          as a cause. Finally, the strong correlation of
                                                                                                                   the DT trend between the troposphere and
   Fig. 3. Monthly mean 300-hPa                                                                                    stratosphere is unnatural.
   bDT¶À, the average day-night tem-                                                                                   We are left to propose that the trends are
   perature difference, at the 10 LKS                                                                              caused by decreases over time in the un-
   tropical stations spanning the                                                                                  corrected heating of the sensor. This is plausi-
   1959 to 1997 period.
                                                                                                                   ble a priori given the history of radiosonde
                                                                                                                   development and improvement efforts and is
                                                                                                                   fully consistent with all characteristics of the
                                                                                                                   trend here documented: strong in the strato-
                                                                                                                   sphere (due mainly to the low thermal dif-
                                                                                                                   fusivity of thin air) and in phase with solar
                                                                                                                   heating. The smaller effect in NH is consistent
                                                                                                                   with the expected superior stability of those
                                                                                                                   stations.
                                                                                                                       The trend reported from a particular set of
                                                                                                                   stations can be adjusted to a nighttime-only
                                                                                                                   value by adding an adjustment dsol equal to the
                                                                                                                   trend in bDT¶À multiplied by a factor f rep-
                                                                                                                   resenting the fraction of the reported trend
   Table 2. Layer-average tropospheric and stratospheric temperature trends (in K per decade) reported by          coming from daytime data (29). This assumes
   LKS for unhomogenized data (‘‘orig’’), and with solar heating bias removed (‘‘new’’). Factor f is specific to   that stations that do not collect nighttime data
   LKS station subset. Uncertainties are 1s sampling uncertainty in the solar heating bias correction only.        are just as susceptible to spurious daytime
                                                                                                                   trends, on average, as those that do.
                                        Tropics                  NH extratropics               SH extratropics         MSU Channel 2 data can be used to test this
                                                                                                                   assumption. We require only trend differences
                                                    1979–1997
                                                                                                                   between sites, which are much more robust to
   f                                     0.84                         0.50                          0.67
   50–100 hPa (orig)                    j1.30                        j0.85                         j1.04           analysis method than the overall MSU trend
   50–100 hPa (new)                  j0.81 T 0.08                 j0.78 T 0.03                  j0.67 T 0.08       itself. We use diurnal-mean MSU trends from
   850–300 hPa (orig)                   j0.02                        þ0.10                         j0.07           the University of Alabama at Huntsville at LKS
   850–300 hPa (new)                 þ0.14 T 0.04                 þ0.14 T 0.02                  þ0.01 T 0.04       station locations (3). Our assumption implies
                                                    1959–1997                                                      that daytime-only stations will cool more
   50–100 hPa (orig)                    j0.71                        j0.43                         j0.50           compared to colocated MSU retrievals than
   50–100 hPa (new)                  j0.52 T 0.06                 j0.38 T 0.02                  j0.30 T 0.07       will twice-daily stations. The calculated dif-
   850–300 hPa (orig)                   þ0.17                        þ0.06                         þ0.25
   850–300 hPa (new)                 þ0.23 T 0.03                 þ0.07 T 0.01                  þ0.30 T 0.03       ferences, given in Table 1 (we combine SH
                                                                                                                   and NH here because there are no daytime-


   Fig. 4. Trend in bDT¶À during
   1979 to 1997 (top) and 1959
   to 1997 (bottom) at LKS
   stations. Green, Tropics (30-N
   to 30-S); red, Southern Hem-
   isphere (90-S to 30-S); blue,
   Northern Hemisphere (30-N
   to 90-N). Error bars are 1s
   sampling uncertainty. Figures
   in parentheses are the number
   of stations used.




1558                                           2 SEPTEMBER 2005 VOL 309               SCIENCE      www.sciencemag.org
                                                                                                                                                              REPORTS
only LKS stations in NH), are fully consist-           References and Notes                                          19. S. Chapman, R. S. Lindzen, Atmospheric Tides (D. Reidel,
                                                    1. B. D. Santer et al., Science 309, 1551 (2005); published          Norwell, MA, 1970).
ent with this assumption, particularly for the                                                                       20. D. R. Easterling et al., Science 277, 364 (1997).
                                                       online 11 August 2005 (10.1126/science.1114867).
tropical stations. In the extratropics there are    2. J. K. Angell, J. Clim. 16, 2288 (2003).                       21. D. J. Gaffen, R. J. Ross, J. Clim. 12, 811 (1999).
only four daytime-only stations so the MSU          3. J. R. Lanzante, S. A. Klein, D. J. Seidel, J. Clim. 16, 241   22. W. J. Randel et al., Science 285, 1689 (1999).
test is less meaningful, but the two indepen-          (2003).                                                       23. K. N. Liou, T. Sasamori, J. Atmos. Sci. 32, 2166 (1975).
                                                    4. D. E. Parker et al., Geophys. Res. Lett. 24, 1499 (1997).     24. R. E. Eskridge et al., Bull. Am. Meteorol. Soc. 76,
dent estimates do agree within 0.03-C per           5. P. W. Thorne et al., J. Geophys. Res., in press.                  1759 (1995).
decade.                                             6. D. H. Douglass, B. D. Pearson, S. F. Singer, P. C.            25. H. Riehl, Tropical Meteorology (McGraw Hill, New
    To illustrate the importance of the heating        Knappenberger, P. J. Michaels, Geophys. Res. Lett. 31,            York, 1954).
                                                       L13207 (2004).                                                26. S. C. Sherwood, Geophys. Res. Lett. 27, 3525 (2000).
bias, we have computed its impact dsol on the       7. D. J. Gaffen et al., Science 287, 1242 (2000).                27. J. R. Christy, R. W. Spencer, W. B. Norris, W. D.
trends at LKS stations. The LKS f factors,          8. D. E. Parker, D. I. Cox, Int. J. Climatol. 15, 473                Braswell, D. E. Parker, J. Atmos. Oceanic Technol. 20,
unhomogenized trends, and trends adjusted              (1995).                                                           613 (2003).
                                                    9. M. Free, D. J. Seidel, J. Geophys. Res. 110, D07101           28. T. Sasamori, J. London, J. Atmos. Sci. 23, 543 (1966).
only for solar heating are given for the middle                                                                      29. Data files and further information on methods, uncer-
                                                       (2005).
troposphere and lower stratosphere in Table 2.     10. J. K. Luers, R. E. Eskridge, J. Appl. Meteorol. 34, 1241          tainty, and interpretation of our results are available as
In the stratosphere, our dsol is similar to the        (1995).                                                           supporting material on Science Online.
                                                   11. I. Durre, T. C. Peterson, R. S. Vose, J. Clim. 15, 1335       30. S.C.S. thanks J. Risbey and K. Braganza for useful dis-
total adjustments by LKS and others, with                                                                                cussions. This work was supported by the National
                                                       (2002).
trends moving closer to those from MSU (13).       12. L. Haimberger, ‘‘Homogenization of radiosonde temper-             Oceanic and Atmospheric Administration Climate and
At the tropical tropopause (of relevance to            ature time series using ERA-40 analysis feedback                  Global Change Program award NA03OAR4310153, and
                                                       information,’’ Tech. Rep. European Center for Medium              by NSF ATM-0134893.
stratospheric water vapor), dsol is somewhat
                                                       Range Weather Forecasting (2005), ERA-40 Project
smaller than LKS_s. In the troposphere, how-           Report Series 23.                                             Supporting Online Material
ever, dsol is much larger than previous adjust-    13. D. J. Seidel et al., J. Clim. 17, 2225 (2004).                www.sciencemag.org/cgi/content/full/1115640/DC1
ments. Indeed, the tropical trend with this        14. P. R. Krishnaiah, B. Q. Miao, Handbook of Statistics,         Methods
                                                       P. R. Krishnaiah, C. R. Rao, Eds. (Elsevier, New York,        SOM Text
adjustment (0.14-C per decade over 1979 to             1988), vol. 7.                                                Data files
1997) would be consistent with model simu-         15. M. Free et al., Bull. Am. Meteorol. Soc. 83, 891 (2002).      References and Notes
lations driven by observed surface warming,        16. W. J. Randel, F. Wu, in preparation.
which was not true previously (1). One inde-       17. D. J. Seidel, M. Free, J. Wang, J. Geophys. Res. 110,         2 June 2005; accepted 27 July 2005
                                                       D09102 (2005).                                                Published online 11 August 2005;
pendent indication that the solar-adjusted         18. A. Dai, K. E. Trenberth, T. R. Karl, J. Clim. 12, 2451        10.1126/science.1115640
trends should be more accurate is their con-           (1999).                                                       Include this information when citing this paper.
sistency across latitude belts: for the period
1979 to 1997, the spread of values fell by
70% in the lower stratosphere and 25% in
the troposphere.
                                                             The Transcriptional Landscape of
    Though this is encouraging, our confidence
in these nighttime trends is still limited given                 the Mammalian Genome
that other radiosonde errors have not been
addressed. SH trends from 1958 to 1997 seem                      The FANTOM Consortium* and RIKEN Genome Exploration
unrealistically high in the troposphere, espe-                         Research Group and Genome Science Group
cially with the dsol adjustment, although this                           (Genome Network Project Core Group)*
belt has by far the worst sampling. Previous
homogenization efforts typically produced                   This study describes comprehensive polling of transcription start and
small changes to mean tropospheric trends,                  termination sites and analysis of previously unidentified full-length comple-
which could mean that other error trends                    mentary DNAs derived from the mouse genome. We identify the 5¶ and 3¶
cancel out dsol in the troposphere. In our judg-            boundaries of 181,047 transcripts with extensive variation in transcripts arising
ment, however, such fortuitous cancellation of              from alternative promoter usage, splicing, and polyadenylation. There are
independent errors is unlikely compared to the              16,247 new mouse protein-coding transcripts, including 5154 encoding
possibility that most solar artifacts were pre-             previously unidentified proteins. Genomic mapping of the transcriptome reveals
viously either missed or their removal negated              transcriptional forests, with overlapping transcription on both strands,
by other, inaccurate adjustments. To be de-                 separated by deserts in which few transcripts are observed. The data provide
tected easily, a shift must be large and abrupt,            a comprehensive platform for the comparative analysis of mammalian
but dsol was spread out over so many stations               transcriptional regulation in differentiation and development.
(79% of stations during 1979 to 1997 and
90% during 1959 to 1997 experienced DT             The production of RNA from genomic DNA                            ation and termination sites (2, 3). A detailed
trends significant at 95% level), at such          is directed by sequences that determine the                       description of the data sets generated, mapping
modest levels, and of sufficient frequency at      start and end of transcripts and splicing into                    strategies, and depth of coverage of the mouse
many stations that many may have been              mature RNAs. We refer to the pattern of tran-                     transcriptome is provided in supporting online
undetectable. Most important, jumps in the         scription control signals, and the transcripts                    material (SOM) text 1 (Tables 1 and 2). We
difference between daytime and nighttime           they generate, as the transcriptional landscape.                  have identified paired initiation and termi-
monthly means would be detectable at only a        To describe the transcriptional landscape of                      nation sites, the boundaries of independent
few tropical stations because most lack suffi-     the mammalian genome, we combined full-                           transcripts, for 181,047 independent tran-
cient nighttime data. In any case, we conclude     length cDNA isolation (1) and 5¶- and 3¶-end                      scripts in the transcriptome (Table 3). In
that carefully extracted diurnal temperature       sequencing of cloned cDNAs, with new cap-                         total, we found 1.32 5¶ start sites for each 3¶
variations can be a valuable troubleshooting       analysis gene expression (CAGE) and gene                          end and 1.83 3¶ ends for each 5¶ end (table
diagnostic for climate records, and that the       identification signature (GIS) and gene sig-                      S1). Based on these data, the number of
uncertainty in late–20th century radiosonde        nature cloning (GSC) ditag technologies for                       transcripts is at least one order of magnitude
trends is large enough to accommodate the          the identification of RNA and mRNA se-                            larger than the estimated 22,000 Bgenes[ in
reported surface warming.                          quences corresponding to transcription initi-                     the mouse genome (4) (SOM text 1), and the

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