This package provides time course gene expression datasets. The data included in the package and its processing is described below.
Overview of the datasets included in timecoursedata:
| object | description |
|---|---|
shoemaker2015 |
microarray data from influenza-exposed mice |
varoquaux2019leaf |
RNA-seq from leaf samples of S. bicolor exposed to drought |
varoquaux2019root |
RNA-seq from root samples of S. bicolor exposed to drought |
Each datasets in this package are represented by:
All datasets can also be loaded as SummarizedExperiment objects using the following functions:
| name | matrix/data.frame | SummarizedExperiment |
|---|---|---|
shoemaker2015 |
data(shoemaker2015) |
load_shoemaker2015() |
varoquaux2019leaf |
data(varoquaux2019leaf) |
load_varoquaux2019(sample_type="leaf") |
varoquaux2019root |
data(varoquaux2019root) |
load_varoquaux2019(sample_type="root") |
The metadata contains at least the following information:
| column | description |
|---|---|
row.names |
name of the sample |
Timepoint |
which timepoints this sample belongs to |
Group |
which group this sample belongs to |
Replicate (optional) |
which replicate this sample belongs to |
This dataset is a microarray time-course experiment, exposing mice to three different strains of influenza with varying doses. The authors of the experiment collected three replicates of lung tissue samples during 14 unevenly-spaced time-points after infection, resulting in a dataset of 209 samples.
library(timecoursedata)
## Loading required package: SummarizedExperiment
## Loading required package: MatrixGenerics
## Loading required package: matrixStats
##
## Attaching package: 'MatrixGenerics'
## The following objects are masked from 'package:matrixStats':
##
## colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
## colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
## colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
## colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
## colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
## colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
## colWeightedMeans, colWeightedMedians, colWeightedSds,
## colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
## rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
## rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
## rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
## rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
## rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
## rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
## rowWeightedSds, rowWeightedVars
## Loading required package: GenomicRanges
## Loading required package: stats4
## Loading required package: BiocGenerics
##
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
##
## Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
## as.data.frame, basename, cbind, colnames, dirname, do.call,
## duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
## lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
## pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
## tapply, union, unique, unsplit, which.max, which.min
## Loading required package: S4Vectors
##
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:utils':
##
## findMatches
## The following objects are masked from 'package:base':
##
## I, expand.grid, unname
## Loading required package: IRanges
## Loading required package: GenomeInfoDb
## Loading required package: Biobase
## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
##
## Attaching package: 'Biobase'
## The following object is masked from 'package:MatrixGenerics':
##
## rowMedians
## The following objects are masked from 'package:matrixStats':
##
## anyMissing, rowMedians
data(shoemaker2015)
head(shoemaker2015$meta)
## Group Replicate Timepoint
## GSM1557140 0 K 1 0
## GSM1557141 1 K 2 0
## GSM1557142 2 K 3 0
## GSM1557143 3 K 1 12
## GSM1557144 4 K 2 12
## GSM1557145 5 K 3 12
head(shoemaker2015$data)
## GSM1557140 GSM1557141 GSM1557142 GSM1557143 GSM1557144
## NM_009912 4.364173 4.338212 4.467095 4.096020 4.047477
## NM_008725 8.227778 8.318347 8.763661 8.894427 8.940470
## NM_007473 4.656177 5.010798 5.134367 4.651378 4.148347
## ENSMUST00000094955 5.845917 5.631973 5.689894 5.737804 5.855101
## NM_001042489 10.527553 10.391772 10.545010 10.643843 10.748155
## NM_008159 5.178836 4.961242 4.968316 5.008923 5.086048
## GSM1557145 GSM1557146 GSM1557147 GSM1557148 GSM1557149
## NM_009912 4.434741 4.423124 4.269806 4.340769 4.459663
## NM_008725 7.503926 8.050293 10.494730 7.824772 10.058947
## NM_007473 4.738783 4.602129 4.668651 4.496141 4.769481
## ENSMUST00000094955 5.600944 5.995875 5.619528 5.445811 5.990237
## NM_001042489 10.850465 10.862142 10.863667 10.863092 10.726463
## NM_008159 4.952627 5.301192 5.223774 4.987974 5.431684
## GSM1557150 GSM1557151 GSM1557152 GSM1557153 GSM1557154
## NM_009912 4.075490 4.392139 4.319921 4.036894 4.278102
## NM_008725 7.172212 7.755944 7.539625 10.347932 8.022185
## NM_007473 4.466626 4.730158 4.678658 4.942729 5.142943
## ENSMUST00000094955 5.941696 5.538740 5.532077 5.764879 5.951631
## NM_001042489 11.140806 10.888805 10.695048 10.510220 10.199757
## NM_008159 5.570177 5.444860 5.704597 5.577245 5.563220
## GSM1557155 GSM1557156 GSM1557157 GSM1557158 GSM1557159
## NM_009912 4.229525 4.790464 4.618102 4.292883 4.362999
## NM_008725 9.386234 8.011647 11.435488 11.748686 12.490890
## NM_007473 5.591846 6.111549 6.249046 4.822046 5.347795
## ENSMUST00000094955 5.419838 5.450870 5.644346 5.703008 5.502000
## NM_001042489 10.621972 10.900136 10.203150 10.453638 10.814877
## NM_008159 4.617328 5.680736 5.082844 4.890212 4.525892
## GSM1557160 GSM1557161 GSM1557162 GSM1557163 GSM1557164
## NM_009912 4.487013 4.914105 4.341961 4.706027 5.555682
## NM_008725 10.632376 7.380812 10.595355 7.370605 7.888910
## NM_007473 4.738201 5.238022 5.466100 4.679871 4.421353
## ENSMUST00000094955 5.644760 5.591560 5.727354 5.696933 5.667284
## NM_001042489 10.533647 10.385112 10.540360 10.463027 10.784618
## NM_008159 4.823083 5.172196 5.288532 5.177787 4.999295
## GSM1557165 GSM1557166 GSM1557167 GSM1557168 GSM1557169
## NM_009912 4.745618 4.491622 4.383318 4.777431 4.378846
## NM_008725 12.798337 8.647044 11.393278 11.835689 10.626121
## NM_007473 4.791897 4.287149 4.277924 4.876234 5.130431
## ENSMUST00000094955 5.517760 5.654180 5.754559 5.852834 5.526622
## NM_001042489 10.184721 10.137488 10.400821 11.351745 10.622861
## NM_008159 4.590930 4.798051 4.812678 5.178836 4.857245
## GSM1557170 GSM1557171 GSM1557172 GSM1557173 GSM1557174
## NM_009912 4.171708 4.769544 4.977933 4.560899 4.479142
## NM_008725 9.798396 7.239886 8.279798 12.055871 12.070300
## NM_007473 4.706490 4.475112 4.375857 6.219516 4.947267
## ENSMUST00000094955 6.093310 5.973003 5.788523 5.672030 5.755646
## NM_001042489 10.092476 10.488544 10.392167 10.729901 10.970620
## NM_008159 4.948274 4.769544 4.850561 5.056947 5.032845
## GSM1557175 GSM1557176 GSM1557177 GSM1557178 GSM1557179
## NM_009912 4.825519 5.185680 4.805229 5.054352 4.797555
## NM_008725 11.797380 8.621139 9.281965 10.488918 10.332053
## NM_007473 4.888116 5.222018 6.099391 4.909978 5.118556
## ENSMUST00000094955 5.676086 5.525499 5.662417 5.747861 5.631346
## NM_001042489 10.448382 10.688269 10.565089 10.430214 10.964179
## NM_008159 5.299177 5.258186 4.588135 4.888349 4.467719
## GSM1557180 GSM1557181 GSM1557182 GSM1557183 GSM1557184
## NM_009912 4.591574 5.215763 3.779645 3.814287 3.876829
## NM_008725 7.371657 7.411414 7.336296 8.628212 12.329396
## NM_007473 4.521390 4.591574 4.426017 4.161715 4.660551
## ENSMUST00000094955 5.897702 5.615557 5.429603 5.526809 5.550831
## NM_001042489 10.825507 11.131434 10.326305 10.220033 10.175231
## NM_008159 4.755363 4.887416 4.369025 4.344682 4.154756
## GSM1557185 GSM1557186 GSM1557187 GSM1557188 GSM1557189
## NM_009912 4.119044 4.080191 4.228237 3.703268 3.981815
## NM_008725 8.032115 8.668254 8.038815 13.341029 7.029826
## NM_007473 4.370360 4.857542 4.453454 4.614865 4.300260
## ENSMUST00000094955 5.803437 5.569814 5.608358 5.378740 5.965425
## NM_001042489 10.146251 10.213050 10.436663 10.188191 10.489912
## NM_008159 4.291826 4.531201 4.734511 4.457230 4.879403
## GSM1557190 GSM1557191 GSM1557192 GSM1557193 GSM1557194
## NM_009912 4.896947 4.782898 4.559143 5.039419 4.434821
## NM_008725 9.343783 10.890933 11.795071 11.656627 8.603541
## NM_007473 4.978535 5.186723 5.665412 5.114626 4.539313
## ENSMUST00000094955 5.618791 5.486148 5.465865 5.576377 5.546515
## NM_001042489 10.998721 10.806703 10.567866 10.966331 10.550902
## NM_008159 4.742591 4.985470 4.916281 4.817952 4.856053
## GSM1557195 GSM1557196 GSM1557197 GSM1557198 GSM1557199
## NM_009912 4.349430 5.105131 4.142786 4.052686 3.846554
## NM_008725 8.165527 10.066594 13.111832 9.748929 12.210118
## NM_007473 4.946764 4.594220 4.794573 4.637024 4.464674
## ENSMUST00000094955 6.143985 5.466685 5.749370 5.433921 5.899440
## NM_001042489 10.420457 11.137841 10.392454 10.463301 10.418195
## NM_008159 4.781958 4.972117 4.561630 4.457465 4.604472
## GSM1557200 GSM1557201 GSM1557202 GSM1557203 GSM1557204
## NM_009912 4.483545 4.202688 3.720259 3.798996 4.404255
## NM_008725 7.171576 6.798969 10.518543 13.236289 12.706269
## NM_007473 4.833654 4.734511 4.395918 4.459585 6.682213
## ENSMUST00000094955 6.064716 5.797334 5.757720 5.595886 5.801177
## NM_001042489 10.567606 10.290602 10.330799 10.189672 10.555445
## NM_008159 4.551875 4.642562 4.841079 4.665183 4.775605
## GSM1557205 GSM1557206 GSM1557207 GSM1557208 GSM1557209
## NM_009912 4.186379 3.911534 4.335138 4.351718 3.783410
## NM_008725 14.746318 8.388004 8.329866 11.823550 12.367629
## NM_007473 4.575304 4.287238 6.269483 5.833289 4.783588
## ENSMUST00000094955 5.659962 5.697897 5.582008 5.709882 5.249910
## NM_001042489 10.552405 10.057967 10.469323 10.575399 10.382377
## NM_008159 4.871171 4.412544 4.393864 4.351718 4.293059
## GSM1557210 GSM1557211 GSM1557212 GSM1557213 GSM1557214
## NM_009912 4.428263 4.098843 4.275074 4.498815 4.421997
## NM_008725 12.429596 11.026308 9.778742 9.254200 11.720704
## NM_007473 5.483410 4.715979 4.275074 4.498815 4.347058
## ENSMUST00000094955 5.483410 6.293183 5.616893 5.792576 5.911589
## NM_001042489 10.397636 10.566904 10.517413 10.486989 10.620774
## NM_008159 4.597503 5.036530 4.344002 4.782209 4.850441
## GSM1557215 GSM1557216 GSM1557217 GSM1557218 GSM1557219
## NM_009912 4.278102 4.359977 4.231456 4.382491 4.490164
## NM_008725 9.653914 13.248020 9.389719 12.356165 8.931784
## NM_007473 5.202511 4.727034 5.091679 4.544499 4.451089
## ENSMUST00000094955 5.580062 5.672538 5.710245 5.792888 5.818898
## NM_001042489 10.284228 10.877663 9.807760 10.570610 10.718365
## NM_008159 4.591431 4.626090 4.051229 4.829530 4.821802
## GSM1557220 GSM1557221 GSM1557222 GSM1557223 GSM1557224
## NM_009912 4.451878 4.543759 3.942168 4.714531 4.388271
## NM_008725 10.479656 8.721105 8.193179 9.991749 10.726615
## NM_007473 4.917595 4.515665 4.283783 5.186249 4.758235
## ENSMUST00000094955 5.699193 5.732816 5.740583 5.632390 5.898543
## NM_001042489 10.738015 10.349175 10.739315 10.585906 10.582356
## NM_008159 4.963567 4.791586 4.803562 4.957470 4.549076
## GSM1557225 GSM1557226 GSM1557227 GSM1557228 GSM1557229
## NM_009912 4.566955 4.195827 4.178300 4.479451 4.104872
## NM_008725 10.228634 12.318893 5.659962 5.909207 8.530658
## NM_007473 4.617328 4.944692 4.302535 4.677377 5.833652
## ENSMUST00000094955 6.139950 6.181067 6.185509 6.300034 5.961441
## NM_001042489 10.547606 10.601298 11.348000 11.055633 10.835023
## NM_008159 4.566955 4.833231 4.954521 4.985252 4.539907
## GSM1557230 GSM1557231 GSM1557232 GSM1557233 GSM1557234
## NM_009912 4.338895 4.485318 4.271684 4.596576 3.986399
## NM_008725 8.655709 9.740692 7.706644 11.805003 10.480871
## NM_007473 5.128607 4.932876 4.840597 4.869283 4.662460
## ENSMUST00000094955 5.966530 6.280827 6.109401 6.405668 6.612320
## NM_001042489 10.529988 11.044619 10.811322 11.083515 10.860076
## NM_008159 4.700197 4.902439 5.009781 5.494211 5.426557
## GSM1557235 GSM1557236 GSM1557237 GSM1557238 GSM1557239
## NM_009912 4.616836 4.749216 4.675015 4.273201 5.020403
## NM_008725 8.830427 9.679068 7.362256 7.071915 6.056961
## NM_007473 4.748060 6.905228 4.632717 4.499807 4.622592
## ENSMUST00000094955 6.143179 6.272634 6.532824 5.680097 5.793386
## NM_001042489 11.125786 11.114015 11.462637 10.157125 10.525139
## NM_008159 5.067383 6.146764 6.222246 5.986350 6.043572
## GSM1557240 GSM1557241 GSM1557242 GSM1557243 GSM1557244
## NM_009912 5.251089 4.966550 4.753445 3.941270 4.515665
## NM_008725 10.952893 9.109165 11.171724 12.438175 12.082368
## NM_007473 4.852832 5.357048 4.966219 4.984162 5.262957
## ENSMUST00000094955 5.805906 5.757401 6.151772 6.291113 6.345786
## NM_001042489 10.513729 10.457131 11.096552 10.569988 10.832037
## NM_008159 5.915311 5.857990 4.922212 4.677310 4.729183
## GSM1557245 GSM1557246 GSM1557247 GSM1557248 GSM1557249
## NM_009912 5.665276 6.488279 5.640857 5.882101 5.359026
## NM_008725 7.484742 14.269685 9.547562 6.822269 7.454090
## NM_007473 5.261968 5.724288 5.030260 5.556562 5.547032
## ENSMUST00000094955 5.760461 5.552008 5.720658 5.500171 5.418709
## NM_001042489 9.963723 10.001382 9.372102 9.976429 9.394465
## NM_008159 6.021210 6.758634 5.948449 6.103791 5.440692
## GSM1557250 GSM1557251 GSM1557252 GSM1557253 GSM1557254
## NM_009912 6.404324 4.609924 4.406698 4.368189 5.777961
## NM_008725 7.842379 8.999277 11.320822 11.470111 7.295824
## NM_007473 5.241174 4.966385 4.721615 6.120460 4.991179
## ENSMUST00000094955 5.557186 6.207257 5.773867 5.922330 5.841799
## NM_001042489 9.967169 10.384140 10.724393 10.699444 9.858504
## NM_008159 6.171807 4.942336 4.740721 4.906875 4.852235
## GSM1557255 GSM1557256 GSM1557257 GSM1557258 GSM1557259
## NM_009912 6.741990 5.592597 4.535077 4.554227 4.433064
## NM_008725 10.403716 8.452166 11.171890 12.752098 13.415204
## NM_007473 4.890037 4.692810 5.070211 4.781958 6.381461
## ENSMUST00000094955 5.323305 5.559859 5.843182 6.246366 6.093944
## NM_001042489 9.919964 10.048202 10.777057 10.984228 10.923453
## NM_008159 5.205133 4.894744 4.906875 4.739688 4.762501
## GSM1557260 GSM1557261 GSM1557262 GSM1557263 GSM1557264
## NM_009912 5.495435 5.523324 4.905033 5.503599 5.764879
## NM_008725 7.540585 6.174129 6.468902 7.206698 7.649929
## NM_007473 5.804240 4.491009 4.445790 4.689603 4.542871
## ENSMUST00000094955 5.463873 5.473692 5.254483 5.144017 5.022794
## NM_001042489 10.345236 9.972758 10.379279 10.856363 11.025982
## NM_008159 5.495435 4.874823 5.272055 5.503599 5.494555
## GSM1557265 GSM1557266 GSM1557267 GSM1557268 GSM1557269
## NM_009912 5.939306 3.987378 4.016140 4.362999 4.456915
## NM_008725 8.105093 10.856860 11.028350 5.770169 7.153733
## NM_007473 4.406861 4.747418 5.261294 4.940483 4.869578
## ENSMUST00000094955 5.460192 5.793043 5.992314 5.854356 6.050855
## NM_001042489 10.953786 10.591246 10.117323 10.522285 10.624859
## NM_008159 5.299966 4.291738 4.673393 4.760211 4.728922
## GSM1557270 GSM1557271 GSM1557272 GSM1557273 GSM1557274
## NM_009912 4.024435 4.495147 4.261639 4.117057 4.943234
## NM_008725 6.567563 8.728671 6.848437 6.540968 7.190716
## NM_007473 4.896889 5.013739 4.676230 4.543759 4.418370
## ENSMUST00000094955 6.132760 5.665344 5.861705 5.773677 5.524824
## NM_001042489 10.706000 10.330550 10.946127 10.562018 10.760353
## NM_008159 4.852354 4.670820 4.704770 4.508935 4.773462
## GSM1557275 GSM1557276 GSM1557277 GSM1557278 GSM1557279
## NM_009912 4.306029 4.493309 4.890677 4.576606 4.276678
## NM_008725 6.884850 7.983978 7.191790 7.506519 7.680313
## NM_007473 4.785216 4.805476 4.481461 5.256291 5.327737
## ENSMUST00000094955 6.015085 6.003857 6.008156 5.813015 6.027442
## NM_001042489 10.801883 11.138517 10.740201 10.872072 10.562141
## NM_008159 4.887416 4.892073 4.987539 4.850381 4.598287
## GSM1557280 GSM1557281 GSM1557282 GSM1557283 GSM1557284
## NM_009912 4.253609 5.618791 4.769608 4.915622 4.259928
## NM_008725 7.800147 8.005089 5.994008 6.118522 6.919488
## NM_007473 4.950843 4.023799 4.134163 4.144738 5.300185
## ENSMUST00000094955 5.832623 6.039170 5.869872 5.938405 5.903482
## NM_001042489 11.068374 10.519977 10.615778 10.512477 10.907005
## NM_008159 4.700197 6.189558 6.523698 6.156064 4.823204
## GSM1557285 GSM1557286 GSM1557287 GSM1557288 GSM1557289
## NM_009912 4.234026 4.176488 6.891772 5.346691 5.762242
## NM_008725 7.202261 6.758937 11.773523 8.139015 12.234747
## NM_007473 4.704704 5.033583 4.543759 4.592362 4.854861
## ENSMUST00000094955 5.727060 5.851848 5.805691 5.915711 5.870612
## NM_001042489 10.738422 10.557855 10.166769 9.947642 9.922876
## NM_008159 4.901053 4.675488 6.706266 6.682902 6.596033
## GSM1557290 GSM1557291 GSM1557292 GSM1557293 GSM1557294
## NM_009912 4.076104 4.359136 4.322166 5.891725 6.514570
## NM_008725 8.717734 6.613730 7.469349 6.626995 10.107581
## NM_007473 4.812862 4.635775 4.658639 4.542723 4.751396
## ENSMUST00000094955 5.906937 5.731549 5.901895 6.052494 6.017405
## NM_001042489 10.854057 11.067427 10.589244 9.858614 10.173731
## NM_008159 5.075083 5.075953 4.831350 7.018339 7.170199
## GSM1557295 GSM1557296 GSM1557297 GSM1557298 GSM1557299
## NM_009912 6.425463 4.728987 4.736843 4.955578 5.651985
## NM_008725 7.355484 7.951215 8.239082 8.481296 7.489405
## NM_007473 4.620629 4.677580 4.604472 4.624692 4.595006
## ENSMUST00000094955 6.197058 5.908030 5.836131 5.785648 6.059861
## NM_001042489 9.815571 10.649139 10.872880 10.682476 10.239906
## NM_008159 7.051797 5.929429 5.458467 5.894717 6.438657
## GSM1557300 GSM1557301 GSM1557302 GSM1557303 GSM1557304
## NM_009912 5.366909 5.934206 4.202313 3.974698 4.470994
## NM_008725 6.553279 7.140028 5.760588 7.652478 6.033148
## NM_007473 4.570155 4.131113 4.576461 4.454084 4.829652
## ENSMUST00000094955 6.265965 6.129214 6.000869 5.907800 5.676761
## NM_001042489 9.684611 9.913968 10.550902 9.841509 10.604800
## NM_008159 6.325956 6.779713 4.457073 4.299997 4.406861
## GSM1557305 GSM1557306 GSM1557307 GSM1557308 GSM1557309
## NM_009912 4.132393 4.121029 5.515498 5.352998 5.049671
## NM_008725 7.610869 7.349823 7.758313 7.944175 7.151428
## NM_007473 4.797927 4.783713 5.045287 5.150056 5.256968
## ENSMUST00000094955 5.975089 5.681678 5.532227 5.520808 5.770962
## NM_001042489 10.638098 10.179589 10.371040 10.773311 10.676827
## NM_008159 4.797927 4.229709 6.410749 5.928721 5.461642
## GSM1557310 GSM1557311 GSM1557312 GSM1557313 GSM1557314
## NM_009912 5.895471 6.117553 5.285084 5.779818 6.473009
## NM_008725 8.142710 6.671533 7.826050 7.355347 7.502631
## NM_007473 3.939021 4.378846 3.824067 5.169129 5.155586
## ENSMUST00000094955 6.060482 5.938827 6.155615 5.614993 5.655070
## NM_001042489 9.896207 9.999910 9.707916 10.435800 10.028116
## NM_008159 5.588012 6.017405 6.046708 6.154682 6.089793
## GSM1557315 GSM1557316 GSM1557317 GSM1557318 GSM1557319
## NM_009912 4.894570 6.675795 7.213355 7.448181 4.442302
## NM_008725 8.058749 6.706531 6.931304 8.024846 6.976459
## NM_007473 5.421090 4.210539 4.744202 4.404092 5.456503
## ENSMUST00000094955 5.919225 6.030878 6.261698 6.218404 5.784459
## NM_001042489 11.066946 10.030803 9.910902 10.181236 10.468105
## NM_008159 5.232981 5.594563 5.566030 5.936152 4.679803
## GSM1557320 GSM1557321 GSM1557322 GSM1557323 GSM1557324
## NM_009912 4.741495 4.724817 4.178109 4.348753 4.366517
## NM_008725 7.358227 11.398423 7.343479 6.891888 7.612510
## NM_007473 5.202933 4.724817 4.683505 4.753317 4.829288
## ENSMUST00000094955 5.690228 5.928012 6.050021 5.655689 6.032278
## NM_001042489 10.610505 10.088188 10.323816 10.632239 10.360863
## NM_008159 4.764280 4.790962 4.821130 4.985361 4.769354
## GSM1557325 GSM1557326 GSM1557327 GSM1557328 GSM1557329
## NM_009912 6.086775 6.649592 7.802700 7.559699 7.029615
## NM_008725 10.211881 8.649701 7.935881 7.052052 8.331449
## NM_007473 4.527165 5.182024 5.097034 4.686926 4.440077
## ENSMUST00000094955 5.732880 5.834892 5.827131 5.933839 5.952802
## NM_001042489 9.773700 9.575058 9.983578 9.732743 9.735889
## NM_008159 5.952718 5.259448 5.641030 5.701682 5.648033
## GSM1557330 GSM1557331 GSM1557332 GSM1557333 GSM1557334
## NM_009912 7.145478 4.691341 4.631465 4.735807 4.280324
## NM_008725 7.167500 6.768800 7.260401 7.038833 6.106649
## NM_007473 4.153302 5.367495 5.465982 4.863897 4.561119
## ENSMUST00000094955 5.977967 5.949566 6.030350 6.185082 6.290782
## NM_001042489 9.769932 10.535064 10.754887 10.489776 10.513604
## NM_008159 5.893351 4.835952 4.842163 5.134760 5.005704
## GSM1557335 GSM1557336 GSM1557337 GSM1557338 GSM1557339
## NM_009912 4.499426 4.546346 6.242130 6.939626 6.606063
## NM_008725 6.918804 7.572455 6.700037 7.213355 7.566364
## NM_007473 5.023166 5.020669 4.578850 4.421997 4.527689
## ENSMUST00000094955 6.062187 5.884790 5.817063 5.718890 5.834257
## NM_001042489 10.753943 9.977372 9.945485 9.651664 9.596188
## NM_008159 4.985143 4.696741 5.740454 6.106123 5.269641
## GSM1557340 GSM1557341 GSM1557342 GSM1557343 GSM1557344
## NM_009912 7.447351 7.344817 7.922137 7.726694 7.846047
## NM_008725 7.331975 7.556927 7.303713 7.310386 8.398339
## NM_007473 4.360481 4.475112 4.416028 4.407186 4.713611
## ENSMUST00000094955 5.758677 5.686011 5.758103 5.502533 5.610762
## NM_001042489 9.958154 10.165567 10.163314 10.120078 10.338992
## NM_008159 4.835650 5.749498 5.449370 5.698628 6.032014
## GSM1557345 GSM1557346 GSM1557347 GSM1557348
## NM_009912 8.206850 7.372074 6.531295 7.327079
## NM_008725 7.883068 7.892620 8.579038 7.868487
## NM_007473 4.440872 4.426017 4.786905 4.694543
## ENSMUST00000094955 5.433801 6.073381 5.929202 5.878233
## NM_001042489 9.797462 10.319121 9.178391 10.107715
## NM_008159 5.649718 5.062796 4.856292 4.948274
If you use this dataset, please cite:
@article{shoemaker:ultrasensitive,
author={Shoemaker, J. E. AND Fukuyama, S. AND Eisfeld, A. J. AND Zhao,
Dongming AND Kawakami, Eiryo AND Sakabe, Saori AND Maemura, Tadashi AND Gorai,
Takeo AND Katsura, Hiroaki AND Muramoto, Yukiko AND Watanabe, Shinji AND
Watanabe, Tokiko AND Fuji, Ken AND Matsuoka, Yukiko AND Kitano, Hiroaki AND
Kawaoka, Yoshihiro},
isbn = {1553-7366},
issn = {15537374},
journal = {PLoS Pathogens},
number = {6},
pages = {1--25},
pmid = {26046528},
title = {{An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation}},
volume = {11},
year = {2015},
}
This pairs of datasets (varoquaux2019leaf and varoquaux2019root)
corresponds to transcriptomic data from respectively leaf and root samples of
S. bicolor exposed to droughts (pre-flowering and post-flowering drougt)
from seedling to maturity. Samples were collected weekly during 15 weeks.
The data provided here is not normalized. Please note that the root and leaf
samples were processed and sequenced as two separate batches. Any comparison
between the two datasets should thus be done with care.
data(varoquaux2019leaf)
nrow(varoquaux2019leaf$data)
## [1] 34211
ncol(varoquaux2019leaf$data)
## [1] 197
The metadata associated to these datasets are more complete than the
shoemaker2015 one: it contains 69 fields in total. Amongst the most relevant
are the following:
| column | description |
|---|---|
Block |
The block the plant was grown into. |
Week |
Which week this sample was collected on. |
Genotype |
RTx430 (pre-flowering tolerant) or BTx642 (stay-green postflowering resistant). |
Condition |
Control, preflowering drought, or postflowering drought. |
Day |
Which day this sample was collected on. |
Row |
Which row this plant was grown on. |
No.plants.pooled |
The number of unique plants collected to create this sample. |
Plate |
Sequencing plate. |
For more information, consult the methods and supplementary methods of Varoquaux et al (2019).
If you use these datasets, please cite:
@article{varoquaux:transcriptomic,
author = {Varoquaux, N. and Cole, B. and Gao, C. and Pierroz, G. and Baker, C. R. and Patel, D. and Madera, M. and Jeffers, T. and Hollingsworth, J. and Sievert, J. and Yoshinaga, Y. and Owiti, J. A. and Singan, V. R. and DeGraaf, S. and Xu, L. and Blow, M. J. and Harrison, M. J. and Visel, A. and Jansson, C. and Niyogi, K. K. and Hutmacher, R. and Coleman-Derr, D. and O{\textquoteright}Malley, R. C. and Taylor, J. W. and Dahlberg, J. and Vogel, J. P. and Lemaux, P. G. and Purdom, E.},
title = {Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses},
elocation-id = {201907500},
year = {2019},
doi = {10.1073/pnas.1907500116},
publisher = {National Academy of Sciences},
abstract = {Understanding the molecular response of plants to drought is critical to efforts to improve agricultural yields under increasingly frequent droughts. We grew 2 cultivars of the naturally drought-tolerant food crop sorghum in the field under drought stress. We sequenced the mRNA from weekly samples of these plants, resulting in a molecular profile of drought response over the growing season. We find molecular differences in the 2 cultivars that help explain their differing tolerances to drought and evidence of a disruption in the plant{\textquoteright}s symbiosis with arbuscular mycorrhizal fungi. Our findings are of practical importance for agricultural breeding programs, while the resulting data are a resource for the plant and microbial communities for studying the dynamics of drought response.Drought is the most important environmental stress limiting crop yields. The C4 cereal sorghum [Sorghum bicolor (L.) Moench] is a critical food, forage, and emerging bioenergy crop that is notably drought-tolerant. We conducted a large-scale field experiment, imposing preflowering and postflowering drought stress on 2 genotypes of sorghum across a tightly resolved time series, from plant emergence to postanthesis, resulting in a dataset of nearly 400 transcriptomes. We observed a fast and global transcriptomic response in leaf and root tissues with clear temporal patterns, including modulation of well-known drought pathways. We also identified genotypic differences in core photosynthesis and reactive oxygen species scavenging pathways, highlighting possible mechanisms of drought tolerance and of the delayed senescence, characteristic of the stay-green phenotype. Finally, we discovered a large-scale depletion in the expression of genes critical to arbuscular mycorrhizal (AM) symbiosis, with a corresponding drop in AM fungal mass in the plants{\textquoteright} roots.},
issn = {0027-8424},
URL = {https://www.pnas.org/content/early/2019/12/04/1907500116},
eprint = {https://www.pnas.org/content/early/2019/12/04/1907500116.full.pdf},
journal = {Proceedings of the National Academy of Sciences}
}