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|name=EBF KO HPCs induced to T cell, 00hr00min, biol_rep1
|name=EBF KO HPCs induced to T cell, 00hr00min, biol_rep1
|sample_id=12972
|sample_id=12972
|rna_tube_id=
|rna_tube_id=138H2
|rna_box=138
|rna_box=138
|rna_position=H2
|rna_position=H2
Line 20: Line 20:
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=1.97000
|rna_od260/230=1.97
|rna_od260/280=2.06000
|rna_od260/280=2.06
|sample_cell_type=unclassifiable
|sample_cell_type=unclassifiable
|sample_cell_line=
|sample_cell_line=
Line 29: Line 29:
|rna_sample_type=
|rna_sample_type=
|rna_extraction_protocol=
|rna_extraction_protocol=
|rna_weight_ug=4.20560
|rna_weight_ug=4.21
|rna_concentration=0.15020
|rna_concentration=0.15
|sample_note=
|sample_note=
|profile_hcage=CNhs11058,LSID722,release008,COMPLETED
|profile_hcage=CNhs11058,LSID722,release008,COMPLETED

Revision as of 17:35, 27 February 2012


Name:EBF KO HPCs induced to T cell, 00hr00min, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeunclassifiable
cell lineNA
companyNA
collaborationTomokatsu Ikawa (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs11058

00
10
100
1000
10000
1001-0.0749
1002-0.116
1003-0.129
10040
10050
1006-0.143
1007-0.0529
10080
1009-0.171
1010.166
10100
10110.00572
10120
10130.0747
1014-0.0874
10150.0462
1016-0.344
10170
10180
10190
1020.0411
10200.0411
10210.0672
1022-0.263
10230.113
10240.139
10250
10260
1027-0.048
10280
1029-0.142
103-0.0796
10300
1031-0.973
1032-0.387
10330.113
10340
10350
10360.278
10370
1038-0.377
1039-0.169
1040
1040-0.175
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 no result for this sample


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: CNhs11058

Jaspar motifP-value
MA0002.21.79247e-8
MA0003.10.573
MA0004.10.0417
MA0006.10.972
MA0007.10.356
MA0009.10.767
MA0014.10.545
MA0017.10.538
MA0018.20.951
MA0019.10.893
MA0024.15.31246e-4
MA0025.10.296
MA0027.10.98
MA0028.14.02835e-7
MA0029.10.425
MA0030.10.0424
MA0031.10.865
MA0035.20.571
MA0038.10.0314
MA0039.20.501
MA0040.10.654
MA0041.10.0336
MA0042.10.25
MA0043.10.917
MA0046.17.73929e-14
MA0047.20.448
MA0048.10.134
MA0050.13.64008e-6
MA0051.10.00583
MA0052.10.404
MA0055.10.0828
MA0057.10.934
MA0058.10.0087
MA0059.11.91928e-4
MA0060.10.774
MA0061.10.0295
MA0062.25.37088e-16
MA0065.20.116
MA0066.10.0477
MA0067.10.621
MA0068.10.083
MA0069.10.687
MA0070.10.767
MA0071.10.41
MA0072.10.906
MA0073.10.933
MA0074.10.0977
MA0076.17.86076e-9
MA0077.10.374
MA0078.10.706
MA0079.20.0385
MA0080.21.83773e-12
MA0081.15.85268e-4
MA0083.11.48896e-4
MA0084.10.458
MA0087.10.917
MA0088.10.0476
MA0090.10.0239
MA0091.10.075
MA0092.10.352
MA0093.10.0343
MA0099.20.922
MA0100.10.00108
MA0101.10.0127
MA0102.20.834
MA0103.10.47
MA0104.20.00603
MA0105.11.06413e-4
MA0106.10.0946
MA0107.10.0577
MA0108.21.82599e-6
MA0111.10.498
MA0112.20.00677
MA0113.10.375
MA0114.10.768
MA0115.10.652
MA0116.16.10863e-4
MA0117.10.956
MA0119.10.879
MA0122.10.597
MA0124.10.577
MA0125.10.0856
MA0131.10.257
MA0135.10.0438
MA0136.17.84112e-27
MA0137.21.45639e-4
MA0138.27.02612e-4
MA0139.10.236
MA0140.10.186
MA0141.10.389
MA0142.10.513
MA0143.10.304
MA0144.10.073
MA0145.10.719
MA0146.10.0716
MA0147.10.0024
MA0148.10.449
MA0149.10.099
MA0150.10.283
MA0152.10.995
MA0153.11.35916e-6
MA0154.10.108
MA0155.10.995
MA0156.11.71039e-23
MA0157.10.988
MA0159.10.0236
MA0160.10.389
MA0162.10.258
MA0163.12.43779e-6
MA0164.10.822
MA0258.10.013
MA0259.10.327



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: CNhs11058

Novel motifP-value
10.246
100.0269
1000.824
1010.899
1020.231
1030.16
1040.731
1050.713
1060.667
1070.432
1080.334
1090.0912
110.0662
1100.0573
1110.0207
1120.079
1130.673
1140.752
1150.905
1160.942
1171.51689e-4
1180.0574
1190.67
120.574
1200.374
1210.131
1220.667
1230.57
1240.802
1250.303
1260.242
1270.581
1280.273
1290.416
130.0126
1300.518
1310.911
1320.507
1330.756
1340.314
1350.644
1360.522
1370.0605
1380.616
1390.297
140.589
1400.837
1410.913
1420.498
1430.0781
1440.733
1450.0391
1460.696
1470.531
1480.208
1490.489
150.00918
1500.338
1510.398
1520.826
1530.825
1540.6
1550.242
1560.0542
1570.659
1580.301
1590.359
1600.818
1610.115
1620.331
1630.329
1640.0127
1650.661
1660.513
1670.385
1680.418
1690.0214
170.816
180.277
190.776
20.0854
200.042
210.162
220.684
230.53
240.0686
250.155
260.0134
270.947
280.536
290.01
30.0439
300.134
310.721
320.815
330.34
340.729
350.155
360.0345
370.0676
380.346
390.552
40.805
400.184
410.209
420.168
430.411
440.152
450.597
460.235
470.228
480.114
490.195
50.104
500.638
510.93
520.349
530.457
540.637
550.267
560.792
570.218
580.213
590.803
60.417
600.718
610.107
620.102
630.67
640.423
650.511
660.744
670.809
680.87
690.548
70.217
700.0179
710.00885
720.427
730.0915
740.56
750.0058
760.0831
770.398
780.0807
790.832
80.0385
800.191
810.951
820.825
830.213
840.416
850.716
860.0533
870.167
880.401
890.606
90.917
900.0103
910.918
920.928
930.91
940.161
950.0285
960.173
970.555
980.496
990.329



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: CNhs11058


FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000084 (T cell)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000827 (pro-T cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

FF: FANTOM5
NA

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
NA

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