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FF:13063-139I3

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Name:J2E erythroblastic leukemia response to erythropoietin
Species:Mouse (Mus musculus)
Library ID:CNhs12449
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexNA
ageNA
cell typeerythroblast
cell lineJ2E
companyNA
collaborationPeter Klinken (Western Australian Institute of Medical Research)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)Repurified by minelute

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005952
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12449 CAGE DRX008902 DRR009774
DRR009775
DRR009776
Accession ID Mm9

Library idBAMCTSS
CNhs12449 DRZ001199
DRZ001200
DRZ001201
 DRZ002584
Accession ID Mm10

Library idBAMCTSS
CNhs12449 DRZ012549
DRZ012550
DRZ012551
 DRZ013934
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005952
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10062.ATCACG sRNA-Seq DRX037390 DRR041756
Accession ID Mm9

Library idBAMCTSS
SRhi10062.ATCACG DRZ007365


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs12449

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.0174
10040
1005-0.409
1006-0.143
1007-0.188
10080
1009-0.19
1010.177
10100
10110.165
10120
1013-0.0989
1014-0.0874
10150.128
1016-0.664
10170
10180
10190
1020
10200.827
10210.613
1022-0.0704
10230
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.941
1032-0.32
10330.717
10340
10350
10361.059
10370
1038-0.336
1039-0.222
1040
1040-0.989
10410



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12449

Jaspar motifP-value
MA0002.20.206
MA0003.10.656
MA0004.10.0157
MA0006.10.226
MA0007.10.472
MA0009.10.798
MA0014.10.956
MA0017.10.198
MA0018.20.0826
MA0019.10.617
MA0024.11.41368e-5
MA0025.10.156
MA0027.10.433
MA0028.14.07751e-8
MA0029.10.716
MA0030.10.385
MA0031.10.0491
MA0035.22.19245e-13
MA0038.10.00232
MA0039.20.821
MA0040.10.366
MA0041.10.208
MA0042.10.496
MA0043.10.0265
MA0046.15.41426e-5
MA0047.20.197
MA0048.10.0174
MA0050.19.97103e-4
MA0051.10.0317
MA0052.10.116
MA0055.19.71852e-5
MA0057.10.61
MA0058.10.00554
MA0059.11.37022e-4
MA0060.18.73182e-6
MA0061.10.595
MA0062.21.10015e-10
MA0065.20.0177
MA0066.10.47
MA0067.10.594
MA0068.10.0969
MA0069.10.566
MA0070.10.709
MA0071.10.0817
MA0072.10.797
MA0073.10.9
MA0074.10.316
MA0076.11.64026e-10
MA0077.10.254
MA0078.10.328
MA0079.20.0406
MA0080.20.384
MA0081.10.0344
MA0083.10.0157
MA0084.10.738
MA0087.10.775
MA0088.10.0217
MA0090.10.288
MA0091.10.327
MA0092.10.525
MA0093.10.0172
MA0099.20.0609
MA0100.10.0192
MA0101.10.355
MA0102.20.291
MA0103.10.681
MA0104.29.99737e-5
MA0105.10.0229
MA0106.10.111
MA0107.10.604
MA0108.20.0231
MA0111.10.803
MA0112.20.134
MA0113.10.82
MA0114.10.212
MA0115.10.0154
MA0116.10.0181
MA0117.10.494
MA0119.10.988
MA0122.10.813
MA0124.10.375
MA0125.10.468
MA0131.10.293
MA0135.10.411
MA0136.11.01374e-5
MA0137.20.161
MA0138.20.11
MA0139.10.285
MA0140.12.4696e-22
MA0141.10.0159
MA0142.10.413
MA0143.10.195
MA0144.10.593
MA0145.10.531
MA0146.10.195
MA0147.11.50097e-5
MA0148.10.419
MA0149.10.00813
MA0150.10.0424
MA0152.10.334
MA0153.10.128
MA0154.10.395
MA0155.10.438
MA0156.14.8328e-5
MA0157.10.0175
MA0159.10.0183
MA0160.10.0546
MA0162.10.892
MA0163.13.63783e-4
MA0164.10.467
MA0258.10.266
MA0259.10.0096



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12449

Novel motifP-value
10.166
100.0213
1000.0586
1010.38
1020.239
1030.0686
1040.55
1050.867
1060.61
1070.242
1080.619
1090.0484
110.189
1100.0498
1110.0046
1120.4
1130.242
1140.837
1150.681
1160.166
1173.09957e-4
1180.408
1190.396
120.564
1200.283
1210.456
1220.54
1230.414
1240.0349
1250.0106
1260.061
1270.166
1280.577
1290.815
130.00211
1300.613
1310.458
1320.254
1330.553
1340.0188
1350.075
1360.197
1370.805
1380.464
1390.987
140.578
1400.888
1410.815
1420.227
1430.658
1440.923
1450.103
1460.863
1470.867
1480.131
1490.0552
150.224
1500.372
1510.851
1520.315
1530.638
1540.898
1550.702
1560.262
1570.911
1580.015
1590.944
1600.552
1610.718
1620.721
1630.446
1640.041
1650.883
1660.028
1670.33
1680.803
1690.321
170.963
180.114
190.681
20.12
200.00316
210.195
220.907
230.426
240.28
250.201
260.00992
270.476
280.976
290.0029
30.0876
300.359
310.722
320.656
330.117
340.675
350.49
360.00929
370.283
380.627
390.495
40.318
400.0719
410.104
420.139
430.853
440.357
450.436
460.28
470.352
480.294
490.694
50.439
500.845
510.773
520.098
530.352
540.558
550.0193
560.994
570.158
580.985
590.88
60.801
600.948
610.564
620.422
630.826
640.573
650.894
660.151
670.0599
680.596
690.922
70.156
700.0868
710.00181
720.899
730.286
740.344
750.0332
760.16
770.935
780.102
790.873
80.0642
800.849
810.862
820.548
830.992
840.641
850.792
860.266
870.0894
880.612
890.228
90.523
900.0378
910.683
920.892
930.267
940.527
950.0679
960.445
970.987
980.382
990.411



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12449


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000988 (hematopoietic cell)
0000764 (erythroid lineage cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0002242 (nucleate cell)
0000255 (eukaryotic cell)
0000765 (erythroblast)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
2531 (hematologic cancer)
14566 (disease of cellular proliferation)
0060083 (immune system cancer)
1240 (leukemia)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0100737 (leukemia cell line sample)
0000401 (erythroblastic leukemia cell line sample)
0000350 (experimentally modified sample)
0000344 (0 minute sample)
0000337 (erythropoietin treatment sample)
0000403 (mouse J2E erythroblastic leukemia cell line sample)
0101035 (hematopoietic cell line sample)
0000498 (mouse J2E erythroblastic leukemia line 0min after treatment with erythropoietin sample)

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)

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