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|name=Mouse CD19+ B Cells, donor1
|name=Mouse CD19+ B Cells, donor1
|sample_id=11856
|sample_id=11856
|rna_tube_id=
|rna_tube_id=125A2
|rna_box=125
|rna_box=125
|rna_position=A2
|rna_position=A2
Line 12: Line 12:
|rna_catalog_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL_6
|sample_strain=
|sample_dev_stage=
|sample_dev_stage=
|sample_tissue=spleen
|sample_tissue=spleen
Line 29: Line 29:
|rna_sample_type=total RNA
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_weight_ug=1.32000
|rna_weight_ug=1.32
|rna_concentration=0.02400
|rna_concentration=0.024
|sample_note=
|sample_note=
|profile_hcage=CNhs13531,,,LIBRARY SCHEDULED
|profile_hcage=CNhs13531,LSID1029,release012,COMPLETED
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_srnaseq=,,,

Revision as of 17:48, 27 February 2012


Name:Mouse CD19+ B Cells, donor1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespleen
dev stageNA
sexNA
ageNA
cell typeb cell, CD19+
cell lineNA
companyNA
collaborationKawamoto (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
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

CNhs13531

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.175
10040
10050.0674
1006-0.272
10070.0648
10080
1009-0.19
1010.205
10100
10110.0626
10120
1013-0.129
1014-0.0874
1015-0.119
1016-0.594
10170
10180
10190
1020.337
10200
10210.177
1022-0.208
10230.177
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.0935
103-0.0887
10300.566
1031-0.911
1032-0.728
10330.236
10340
10350
10360.366
10370
1038-0.265
1039-0.0984
1040
1040-0.216
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: CNhs13531

Jaspar motifP-value
MA0002.20.00118
MA0003.10.157
MA0004.10.0329
MA0006.10.705
MA0007.10.816
MA0009.10.592
MA0014.10.741
MA0017.10.986
MA0018.21.80196e-7
MA0019.10.173
MA0024.10.566
MA0025.10.845
MA0027.10.728
MA0028.13.42404e-6
MA0029.10.132
MA0030.10.675
MA0031.10.351
MA0035.20.552
MA0038.10.0618
MA0039.20.734
MA0040.10.529
MA0041.10.0847
MA0042.10.505
MA0043.10.0187
MA0046.11.83514e-12
MA0047.20.979
MA0048.10.377
MA0050.11.80868e-14
MA0051.19.7858e-8
MA0052.10.574
MA0055.10.201
MA0057.10.868
MA0058.10.00467
MA0059.10.00826
MA0060.10.108
MA0061.12.79301e-8
MA0062.21.92873e-17
MA0065.20.573
MA0066.10.128
MA0067.10.00277
MA0068.10.0114
MA0069.10.636
MA0070.10.482
MA0071.10.413
MA0072.10.192
MA0073.10.616
MA0074.10.7
MA0076.16.67479e-7
MA0077.10.339
MA0078.10.674
MA0079.20.0906
MA0080.21.40898e-12
MA0081.13.21903e-4
MA0083.10.0503
MA0084.10.939
MA0087.10.857
MA0088.10.999
MA0090.10.00759
MA0091.10.537
MA0092.10.567
MA0093.10.0256
MA0099.20.707
MA0100.10.193
MA0101.19.86383e-10
MA0102.20.834
MA0103.10.203
MA0104.20.0461
MA0105.13.85152e-8
MA0106.10.906
MA0107.11.34653e-9
MA0108.27.60855e-4
MA0111.10.755
MA0112.20.226
MA0113.10.441
MA0114.10.173
MA0115.10.51
MA0116.10.0185
MA0117.10.102
MA0119.10.171
MA0122.10.913
MA0124.10.816
MA0125.10.0357
MA0131.10.239
MA0135.10.72
MA0136.13.19318e-22
MA0137.20.474
MA0138.20.0203
MA0139.10.853
MA0140.10.803
MA0141.10.847
MA0142.12.82262e-4
MA0143.10.136
MA0144.10.818
MA0145.10.19
MA0146.10.318
MA0147.10.0372
MA0148.10.928
MA0149.10.115
MA0150.10.408
MA0152.10.908
MA0153.19.51782e-9
MA0154.10.0258
MA0155.10.466
MA0156.11.64819e-21
MA0157.10.153
MA0159.10.0388
MA0160.10.808
MA0162.10.976
MA0163.10.00336
MA0164.10.472
MA0258.10.144
MA0259.10.28



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: CNhs13531

Novel motifP-value
10.392
100.0387
1000.607
1010.625
1020.554
1030.278
1040.77
1050.565
1060.563
1070.103
1080.595
1090.351
110.437
1100.176
1110.18
1120.0732
1130.782
1140.431
1150.354
1160.374
1172.30193e-4
1180.1
1190.472
120.48
1200.292
1210.417
1220.945
1230.199
1240.623
1250.149
1260.267
1270.7
1280.365
1290.304
130.0448
1300.986
1310.274
1320.454
1330.802
1340.779
1350.524
1360.858
1370.0368
1380.757
1390.359
140.755
1400.865
1410.283
1420.394
1430.0371
1440.476
1450.259
1460.727
1470.823
1480.106
1490.364
150.184
1500.455
1510.32
1520.506
1530.287
1540.22
1550.301
1560.678
1570.705
1580.0137
1590.818
1600.503
1610.153
1620.0718
1630.083
1640.12
1650.34
1660.56
1670.0886
1680.739
1690.382
170.716
180.28
190.67
20.0307
200.00531
210.351
220.965
230.622
240.67
250.284
260.08
270.474
280.211
290.0431
30.184
300.126
310.541
320.351
330.105
340.403
350.159
360.0583
370.0698
380.776
390.383
40.984
400.187
410.175
420.311
430.35
440.304
450.386
460.469
470.76
480.418
490.169
50.249
500.582
510.778
520.27
530.387
540.626
550.738
560.908
570.81
580.193
590.681
60.633
600.818
610.107
620.0812
630.906
640.983
650.771
660.59
670.822
680.0155
690.646
70.422
700.0283
710.0606
720.354
730.087
740.747
750.00384
760.00325
770.078
780.0706
790.515
80.426
800.0766
810.761
820.43
830.0771
840.711
850.901
860.147
870.519
880.493
890.617
90.992
900.0142
910.958
920.358
930.0622
940.301
950.142
960.322
970.732
980.494
990.0539



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: CNhs13531


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)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000236 (B cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
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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