Data on the short-term effects of removing fetal thymocytes from Notch-Delta interactions

Data compiled from two published studies, Franco et al. 2006 PNAS ("Chris data") and Taghon et al. 2007 Nat. Immunol . ("Mary data")

Mary Data
Gene LZ.DL LZ.ctrl sd.DL sd.ctrl
PU.1 0 -0.0562 0.1366 0.0768
Deltex1 0 -2.3673 0.0973 0.0727
Hes1 0 -0.6637 0.0876 0.0491
pTalpha 0 -1.6962 0.1119 0.0568
Rag.1 0 -0.3275 0.0568 0.0729
CD3g 0 -0.2279 0.0709 0.0461
CD3e 0 -0.3486 0.021 0.0882
Zap70 0 -0.1805 0.1041 0.0147
Lck 0 -0.2936 0.0352 0.0295
Lat 0 -0.3247 0.056 0.1131
Runx3 0 0.0836 0.0589 0.0755
Runx1 0 -0.5068 0.104 0.0454
FOG.1 0 -0.1494 0.0673 0.0533
GATA3b 0 -0.1628 0.1294 0.0803
TCF.7.8 0 -6e-04 0.1068 0.0402
Ets2 0 -0.5775 0.1356 0.0619
Ets1 0 0.0341 0.1022 0.1012
Ikaros 0 -0.0904 0.1351 0.0715
Gfi1 0 -0.2836 0.1234 0.1222
c.Myb 0 -0.2667 0.0225 0.0481
HEBcan 0 -0.2318 0.0675 0.0827
E2A 0 -0.2394 0.1048 0.1528
Id1 0 0.0067 0.0567 0.1098
Id2 0 0.1642 0.111 0.1087
Id3 0 0.3916 0.1266 0.0725
Bcl11b 0 -0.2595 0.1366 0.0742
C.EBPa 0 0.0571 0.1087 0.1499
C.EBPb 0 -0.1034 0.2325 0.2205
         
GATA.1 0 -0.1196 0.1352 0.0202
GATA.2 0 0.1524 0.1327 0.0603
GATA.3.endog 0 -0.1538 0.0801 0.0956
IL7Ra 0 -0.1494 0.0115 0.1334
LEF.1 0 -0.5222 0.13 0.1043
Sox4 0 -0.1819 0.0439 0.0301
Aiolos 0 -0.4102 0.1272 0.2455
Helios 0 0.1786 0.1142 0.1675
Notch1 0 -0.7733 0.0355 0.0434
Notch3 0 -1.0476 0.0467 0.0949
Nrarp 0 -0.4469 0.4878 0.1322
Mitf 0 -0.0353 0.0755 0.0561
CPA3 0 0.0776 0.1075 0.0376
TpoR 0 -0.1113 0.2972 0.2485
SCL 0 -0.2297 0.0589 0.6694
Gfi1B 0 -0.8797 0.1323 0.3406
Mcpt6 0 -0.147 1.3907 1.52
EBF 0 0.1763 0.2693 0.3706
Pax5 0 0.7898 0.4233 0.9294
Hbb.b1 0 0.2142 0.1531 0.0987
EpoR 0 -0.5379 0.1833 0.1134
Nfe2 0 -7e-04 0.1617 0.2169
Fli1 0 0.088 0.0935 0.0628
HoxB4 0 -0.066 0.3987 0.2833
Chris Data
Gene LZ.DL LZ.ctrl LS.SEM
PU.1.coding 0 0.0185 0.0546
Deltex.1 0 -2.376 0.13
HES.1 0 -0.729 0.117
pTalpha 0 -1.299 0.0664
Rag.1 0 -0.0849 0.0869
CD3g 0 -0.0333 0.0276
CD3e 0 -0.0024 0.0466
Zap70 0 0.059 0.127
Lck 0 -0.228 0.0455
LAT 0 -0.162 0.0328
Runx3 0 0.0524 0.0304
Runx1 0 -0.397 0.0453
FOG.1 0 -0.0716 0.0646
GATA.3 0 -0.205 0.129
TCF.1 0 -0.166 0.0621
Ets2 0 -0.388 0.0674
Ets1 0 -0.0094 0.0762
Ikaros 0 0.0932 0.0877
Gfi1 0 -0.188 0.0949
c.Myb 0 -0.253 0.0485
HEBCan 0 0.0029 0.0389
E2A 0 -0.276 0.0834
Id1 0 0.212 0.0575
Id2 0 0.245 0.0664
Id3 0 0.32 0.0684
Bcl11B 0 -0.0028 0.096
C.EBPa 0 0.533 0.246
C.EBPb 0 0.0451 0.0695
       
HEBAlt 0 -1.002 0.144
Bcl11A 0 -0.0939 0.19
PU.1.endog 0 -0.258 0.137
M.CSF.R.rep 0 0.0571 0.233
LysozymeM.repeat 0 0.157 0.216
GM.CSFR.b. 0 -0.131 0.082
Mac.1 0 0.0226 0.035
Egr1 0 0.147 0.218
Egr2 0 -0.0415 0.0947
Egr3 0 -0.718 0.12

Results are expressed as differences between cells grown under normal, T-cell promoting conditions (OP9-DL) and cells deprived of the Notch ligand DL (OP9-control).
All the samples are from retroviral transduction experiments; they are the empty-vector-transduced controls ("Lz"), and so do not precisely represent fresh fetal thymocytes.
All samples were initially cultured without Notch ligands for ~16 hr overnight for introduction of the vectors (Lz for these samples, PU.1 or GATA3 for additional samples in the studies cited) and then split to incubate either in the presence of Notch ligands (DL1) or in the absence of Notch ligands ("cntrl") for an additional 24 hr.

In the Franco et al. experiment, the cells were then sorted for expression of the empty Lz vector and for expression of blood-cell marker CD45 and T-cell marker Thy-1 before RNA was prepared
In the Taghon et al. experiment, the cells were then sorted for expression of the empty Lz vector and for expression of blood-cell marker CD45 only before RNA was prepared; thus some more primitive cells were also included.

All results are log(10) transformed so that no change in expression = 0.