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{{f5samples
{{f5samples
|id=FF:12162-128H2
|id=FF:12162-128H2
|name=MDSC (MC1+Gr1+) control, biol_rep2 (0127 PBS)
|name=MC1+Gr1+ myeloid-derived suppressor cells control, donor2 (0127 PBS)
|sample_id=12162
|sample_id=12162
|rna_tube_id=128H2
|rna_tube_id=128H2
Line 19: Line 19:
|sample_age=
|sample_age=
|sample_ethnicity=
|sample_ethnicity=
|rna_rin=10.00000
|rna_rin=10
|rna_od260/230=
|rna_od260/230=
|rna_od260/280=1.80000
|rna_od260/280=1.8
|sample_cell_type=stem cell
|sample_cell_type=stem cell
|sample_cell_line=
|sample_cell_line=
Line 29: Line 29:
|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=
|rna_extraction_protocol=
|rna_weight_ug=0.59700
|rna_weight_ug=0.597
|rna_concentration=0.03000
|rna_concentration=0.03
|sample_note=
|sample_note=
|profile_hcage=CNhs12541,LSID920,release012,COMPLETED
|profile_hcage=CNhs12541,LSID920,release012,COMPLETED

Revision as of 17:42, 27 February 2012


Name:MC1+Gr1+ myeloid-derived suppressor cells control, donor2 (0127 PBS)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuebone marrow
dev stageNA
sexNA
ageNA
cell typestem cell
cell lineNA
companyNA
collaborationHozumi Motohashi (Tohoku University Graduate School of Medicine)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
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

CNhs12541

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10051.123
1006-0.143
1007-0.0237
10080
1009-0.2
101-0.449
10100
1011-0.108
10120
1013-0.0308
1014-0.0874
1015-0.328
1016-0.594
10170
10180
10190
1020
10200
1021-0.0487
1022-0.315
10230.811
1024-0.0899
1025-0.0611
10260
1027-0.048
10280
1029-0.115
103-0.0887
10300
1031-0.911
1032-0.951
1033-0.0665
10340
10350
10360.0433
10370
1038-0.612
1039-0.595
1040
1040-0.333
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: CNhs12541

Jaspar motifP-value
MA0002.27.11289e-13
MA0003.10.88
MA0004.10.548
MA0006.10.216
MA0007.10.377
MA0009.10.672
MA0014.10.242
MA0017.10.34
MA0018.20.0637
MA0019.10.718
MA0024.10.208
MA0025.10.0203
MA0027.10.657
MA0028.19.84036e-4
MA0029.10.612
MA0030.10.855
MA0031.10.0304
MA0035.20.613
MA0038.10.0357
MA0039.20.0693
MA0040.10.0817
MA0041.10.351
MA0042.10.92
MA0043.11.37283e-4
MA0046.14.89705e-10
MA0047.20.0341
MA0048.10.197
MA0050.15.86115e-5
MA0051.19.88993e-4
MA0052.10.0359
MA0055.10.261
MA0057.10.833
MA0058.10.726
MA0059.10.441
MA0060.10.0608
MA0061.10.00546
MA0062.21.10006e-15
MA0065.20.18
MA0066.10.0947
MA0067.10.0096
MA0068.10.19
MA0069.10.486
MA0070.10.23
MA0071.10.221
MA0072.10.0867
MA0073.10.705
MA0074.10.475
MA0076.15.51876e-4
MA0077.10.151
MA0078.10.759
MA0079.20.378
MA0080.27.90603e-16
MA0081.12.124e-4
MA0083.10.833
MA0084.10.798
MA0087.10.431
MA0088.10.696
MA0090.10.0482
MA0091.10.724
MA0092.10.498
MA0093.10.539
MA0099.20.00144
MA0100.10.061
MA0101.10.0295
MA0102.21.12191e-9
MA0103.10.725
MA0104.20.0567
MA0105.14.9047e-5
MA0106.10.719
MA0107.10.0094
MA0108.20.0571
MA0111.10.469
MA0112.23.44388e-4
MA0113.10.348
MA0114.10.835
MA0115.10.443
MA0116.17.67015e-4
MA0117.10.109
MA0119.10.441
MA0122.10.564
MA0124.10.738
MA0125.10.0224
MA0131.10.807
MA0135.10.418
MA0136.18.83747e-30
MA0137.20.115
MA0138.20.146
MA0139.10.559
MA0140.10.914
MA0141.10.218
MA0142.10.136
MA0143.10.184
MA0144.10.129
MA0145.10.243
MA0146.10.0873
MA0147.10.0487
MA0148.10.103
MA0149.10.315
MA0150.18.40448e-6
MA0152.10.334
MA0153.10.00828
MA0154.10.0294
MA0155.10.895
MA0156.14.12708e-25
MA0157.10.0986
MA0159.10.0145
MA0160.10.212
MA0162.10.571
MA0163.10.0246
MA0164.10.648
MA0258.10.00517
MA0259.10.362



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: CNhs12541

Novel motifP-value
10.172
100.0492
1000.756
1010.766
1020.488
1030.317
1040.635
1050.427
1060.0339
1070.623
1080.855
1090.0686
110.0897
1100.251
1110.527
1120.0405
1130.72
1140.0611
1150.797
1160.954
1177.35746e-4
1180.461
1190.328
120.499
1200.0431
1210.393
1220.412
1230.441
1240.7
1250.157
1260.39
1270.306
1280.0848
1290.35
130.113
1300.623
1310.935
1320.827
1330.0357
1340.833
1350.506
1360.561
1370.041
1380.327
1390.0519
140.295
1400.657
1410.571
1420.00475
1430.00204
1440.791
1450.123
1460.882
1470.748
1480.158
1490.917
150.0463
1500.339
1510.176
1520.258
1530.175
1540.947
1550.551
1560.863
1570.791
1580.022
1590.574
1600.939
1610.132
1620.609
1630.26
1640.04
1650.16
1660.717
1670.808
1680.298
1690.00918
170.172
180.131
190.41
20.403
200.0551
210.505
220.359
230.107
240.239
250.266
260.125
270.746
280.0973
290.026
30.0665
300.448
310.711
320.915
330.261
340.811
350.463
360.1
370.0863
380.294
390.823
40.639
400.176
410.0127
420.265
430.109
440.793
450.811
460.311
470.336
480.241
490.0764
50.131
500.675
510.736
520.927
530.805
540.633
550.629
560.26
570.709
580.178
590.468
60.781
600.225
610.269
620.0788
630.645
640.584
650.245
660.741
670.206
680.772
690.393
70.139
700.0492
710.053
720.27
730.042
740.0595
750.00481
760.213
770.935
780.11
790.874
80.466
800.0523
810.503
820.414
830.228
840.765
850.116
860.0657
870.278
880.533
890.722
90.508
900.154
910.466
920.393
930.235
940.0671
950.0217
960.777
970.94
980.331
990.128



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: CNhs12541


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)
0000048 (multi fate stem cell)
0000355 (multi-potent skeletal muscle stem cell)
0000723 (somatic stem cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000119 (cell layer)
0000383 (musculature of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000486 (multilaminar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001015 (musculature)
0001062 (anatomical entity)
0001134 (skeletal muscle tissue)
0002036 (striated muscle tissue)
0002050 (embryonic structure)
0002204 (musculoskeletal system)
0002329 (somite)
0002385 (muscle tissue)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003077 (paraxial mesoderm)
0003082 (myotome)
0003104 (mesenchyme)
0004120 (mesoderm-derived structure)
0004290 (dermomyotome)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0009142 (entire embryonic mesenchyme)

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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