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|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=1.63000
|rna_od260/230=1.63
|rna_od260/280=1.99000
|rna_od260/280=1.99
|sample_cell_type=stem cell
|sample_cell_type=stem cell
|sample_cell_line=
|sample_cell_line=
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|rna_sample_type=
|rna_sample_type=
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=2.49210
|rna_weight_ug=2.4921
|rna_concentration=0.09230
|rna_concentration=0.0923
|sample_note=
|sample_note=
|profile_hcage=CNhs12556,LSID921,release012,COMPLETED
|profile_hcage=CNhs12556,LSID921,release012,COMPLETED

Revision as of 17:40, 27 February 2012


Name:Lgr5 positive intestinal stem cells, pool2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesmall intestine
dev stageNA
sexfemale
ageNA
cell typestem cell
cell lineNA
companyNA
collaborationMarc van de Wetering
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-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

CNhs12556

00
10
100
1000
1000-0.0355
1001-0.0668
1002-0.116
1003-0.123
10040
10050.108
1006-0.2
1007-0.204
10081.787
1009-0.19
1010.128
10100
1011-0.255
10120
10130.0769
1014-0.0874
1015-0.236
1016-0.465
10170
10180.5
10190
1020
10200
10210
10220.125
10230
1024-0.14
1025-0.0611
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-0.93
10320.415
10330.26
10340
10350
10360.387
10370
1038-0.158
10390.193
1040
1040-0.936
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: CNhs12556

Jaspar motifP-value
MA0002.20.176
MA0003.10.739
MA0004.10.0466
MA0006.10.906
MA0007.10.106
MA0009.10.266
MA0014.10.123
MA0017.11.2258e-14
MA0018.20.0243
MA0019.10.647
MA0024.11.45434e-4
MA0025.10.126
MA0027.10.262
MA0028.13.36025e-7
MA0029.10.123
MA0030.10.923
MA0031.10.547
MA0035.25.7974e-4
MA0038.10.483
MA0039.20.00477
MA0040.10.0352
MA0041.10.179
MA0042.10.364
MA0043.10.0122
MA0046.16.47713e-38
MA0047.20.00318
MA0048.10.0238
MA0050.10.0319
MA0051.10.0233
MA0052.10.00304
MA0055.14.85488e-4
MA0057.10.207
MA0058.10.0422
MA0059.17.03105e-4
MA0060.12.08378e-4
MA0061.10.32
MA0062.24.0465e-9
MA0065.22.38691e-7
MA0066.10.499
MA0067.10.791
MA0068.10.641
MA0069.10.349
MA0070.10.425
MA0071.10.0154
MA0072.10.626
MA0073.10.958
MA0074.10.514
MA0076.12.22101e-6
MA0077.10.359
MA0078.10.173
MA0079.20.105
MA0080.20.00282
MA0081.10.962
MA0083.10.00464
MA0084.10.0702
MA0087.10.0927
MA0088.10.00983
MA0090.10.845
MA0091.10.704
MA0092.10.556
MA0093.10.0526
MA0099.20.0896
MA0100.10.116
MA0101.10.0736
MA0102.20.521
MA0103.14.44e-6
MA0104.20.0138
MA0105.10.0718
MA0106.10.294
MA0107.10.248
MA0108.20.818
MA0111.10.832
MA0112.20.0178
MA0113.10.09
MA0114.17.01781e-16
MA0115.12.28165e-9
MA0116.10.0589
MA0117.10.954
MA0119.10.224
MA0122.10.399
MA0124.10.685
MA0125.10.186
MA0131.10.167
MA0135.10.725
MA0136.11.1514e-9
MA0137.22.29938e-5
MA0138.20.25
MA0139.10.0776
MA0140.10.208
MA0141.11.51017e-5
MA0142.10.151
MA0143.10.457
MA0144.10.00436
MA0145.10.558
MA0146.10.33
MA0147.10.00257
MA0148.10.00193
MA0149.10.00401
MA0150.10.323
MA0152.10.262
MA0153.18.25846e-29
MA0154.10.52
MA0155.10.71
MA0156.13.15287e-6
MA0157.10.93
MA0159.15.253e-4
MA0160.11.47013e-4
MA0162.10.652
MA0163.10.00542
MA0164.10.981
MA0258.10.0796
MA0259.10.115



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: CNhs12556

Novel motifP-value
10.195
100.0393
1000.34
1010.426
1020.816
1030.127
1040.897
1050.435
1060.306
1070.742
1080.617
1090.0164
110.155
1100.105
1110.113
1120.0688
1130.0915
1140.932
1150.615
1160.523
1170.017
1180.397
1190.61
121
1200.842
1210.527
1220.572
1230.0149
1240.0264
1250.0379
1260.00424
1270.429
1280.815
1290.593
132.22926e-6
1300.408
1310.678
1320.658
1330.751
1340.468
1350.085
1360.015
1370.707
1380.277
1390.711
140.842
1400.414
1410.849
1420.755
1430.105
1440.0322
1450.0149
1460.314
1470.824
1480.719
1490.382
150.179
1500.469
1510.861
1520.519
1530.798
1540.73
1550.756
1560.177
1570.467
1580.443
1590.748
1600.565
1610.268
1620.377
1630.727
1640.036
1650.115
1660.512
1670.206
1680.814
1690.0843
170.128
180.38
190.851
20.362
200.119
210.895
220.877
230.311
240.0725
250.166
266.30996e-4
270.912
280.995
290.00184
30.255
300.831
310.54
320.699
330.042
340.662
350.625
360.117
370.185
380.493
390.367
40.366
400.069
410.181
420.693
430.792
440.437
450.918
460.201
470.371
480.187
490.614
50.817
500.982
510.805
520.677
530.491
540.96
550.393
560.888
570.696
580.238
590.944
60.422
600.169
610.246
620.204
630.293
640.473
650.5
660.446
670.977
680.975
690.347
70.02
700.0561
710.0168
720.335
730.0925
740.933
750.0102
760.362
770.496
780.032
790.442
80.0725
800.757
810.814
820.77
830.268
840.767
850.574
860.425
870.014
880.502
890.681
90.675
900.0197
910.264
920.642
930.154
940.878
950.0021
960.332
970.914
980.305
990.421



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: CNhs12556


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)
0000066 (epithelial cell)
0000223 (endodermal cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000723 (somatic stem cell)
0002076 (endo-epithelial cell)
0002250 (intestinal crypt stem cell)
0002251 (epithelial cell of alimentary canal)
0002321 (embryonic cell)
0002371 (somatic cell)
0002563 (intestinal epithelial cell)

UBERON: Anatomy
0000060 (anatomical wall)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000119 (cell layer)
0000160 (intestine)
0000344 (mucosa)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000485 (simple columnar epithelium)
0000490 (unilaminar epithelium)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0001007 (digestive system)
0001062 (anatomical entity)
0001242 (intestinal mucosa)
0001262 (wall of intestine)
0001277 (intestinal epithelium)
0001555 (digestive tract)
0002050 (embryonic structure)
0002532 (epiblast (generic))
0003350 (epithelium of mucosa)
0003929 (gut epithelium)
0004119 (endoderm-derived structure)
0004185 (endodermal part of digestive tract)
0004786 (gastrointestinal system mucosa)
0004808 (gastrointestinal system epithelium)
0004921 (subdivision of digestive tract)
0004923 (organ component layer)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0005911 (endo-epithelium)
0007026 (primitive gut)

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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