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|rna_box=129
|rna_box=129
|rna_position=F7
|rna_position=F7
|sample_cell_lot=10122010.00000
|sample_cell_lot=10122010
|sample_cell_catalog=
|sample_cell_catalog=
|sample_company=
|sample_company=
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|sample_ethnicity=
|sample_ethnicity=
|rna_rin=
|rna_rin=
|rna_od260/230=0.83000
|rna_od260/230=0.83
|rna_od260/280=2.05000
|rna_od260/280=2.05
|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=1.75230
|rna_weight_ug=1.7523
|rna_concentration=0.06490
|rna_concentration=0.0649
|sample_note=
|sample_note=
|profile_hcage=CNhs12557,LSID921,release012,COMPLETED
|profile_hcage=CNhs12557,LSID921,release012,COMPLETED

Revision as of 17:40, 27 February 2012


Name:Lgr5 positive intestinal stem cells, pool3
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

CNhs12557

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.143
10040
10050.0807
1006-0.147
1007-0.125
10081.102
1009-0.19
1010.128
10100
1011-0.188
10120
10130.021
1014-0.0874
1015-0.164
1016-0.465
10170
10180.259
10190
1020
10200
10210
10220.111
10230
1024-0.14
1025-0.00846
10260
1027-0.048
10280
1029-0.176
103-0.0887
10300
1031-1.044
10320.317
10330.436
10340
10350
10360.494
10370
1038-0.101
10390.177
1040
1040-0.711
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: CNhs12557

Jaspar motifP-value
MA0002.20.446
MA0003.10.845
MA0004.10.00816
MA0006.10.943
MA0007.10.101
MA0009.10.232
MA0014.10.0715
MA0017.12.29387e-12
MA0018.21.5081e-6
MA0019.10.608
MA0024.14.29108e-6
MA0025.10.0145
MA0027.10.152
MA0028.15.33992e-9
MA0029.10.166
MA0030.10.351
MA0031.10.142
MA0035.23.97469e-4
MA0038.10.11
MA0039.29.44534e-5
MA0040.10.0404
MA0041.10.157
MA0042.10.437
MA0043.12.92303e-6
MA0046.11.73143e-42
MA0047.24.19068e-4
MA0048.10.00723
MA0050.10.00743
MA0051.10.00513
MA0052.10.327
MA0055.11.02517e-4
MA0057.10.185
MA0058.10.00712
MA0059.18.90678e-4
MA0060.15.88688e-11
MA0061.10.34
MA0062.22.24426e-11
MA0065.23.50076e-6
MA0066.10.996
MA0067.10.154
MA0068.10.816
MA0069.10.459
MA0070.10.644
MA0071.10.0642
MA0072.10.662
MA0073.10.99
MA0074.10.801
MA0076.14.75925e-8
MA0077.10.219
MA0078.10.257
MA0079.20.334
MA0080.20.00215
MA0081.10.715
MA0083.10.584
MA0084.10.0311
MA0087.10.171
MA0088.10.0288
MA0090.10.991
MA0091.10.174
MA0092.10.198
MA0093.10.00962
MA0099.20.0411
MA0100.10.134
MA0101.10.0267
MA0102.20.645
MA0103.15.82553e-6
MA0104.20.00918
MA0105.10.376
MA0106.10.459
MA0107.10.087
MA0108.20.0137
MA0111.10.486
MA0112.20.217
MA0113.10.44
MA0114.13.58103e-15
MA0115.13.72874e-8
MA0116.10.216
MA0117.10.736
MA0119.10.606
MA0122.10.225
MA0124.10.54
MA0125.10.594
MA0131.10.101
MA0135.10.41
MA0136.11.07295e-9
MA0137.21.19763e-4
MA0138.20.0505
MA0139.10.141
MA0140.10.327
MA0141.16.68314e-4
MA0142.10.0675
MA0143.10.109
MA0144.10.011
MA0145.10.712
MA0146.10.314
MA0147.10.00209
MA0148.10.00101
MA0149.10.00909
MA0150.10.305
MA0152.10.342
MA0153.19.95202e-31
MA0154.10.823
MA0155.10.451
MA0156.16.5807e-7
MA0157.10.746
MA0159.10.00361
MA0160.13.93888e-4
MA0162.10.947
MA0163.10.0603
MA0164.10.767
MA0258.10.385
MA0259.10.0898



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: CNhs12557

Novel motifP-value
10.437
100.0671
1000.33
1010.169
1020.952
1030.681
1040.953
1050.481
1060.413
1070.754
1080.683
1090.0564
110.339
1100.146
1110.223
1120.16
1130.0646
1140.444
1150.471
1160.961
1170.0144
1180.642
1190.987
120.903
1200.624
1210.344
1220.879
1230.0103
1240.072
1250.0235
1260.00724
1270.532
1280.946
1290.915
132.53855e-7
1300.422
1310.939
1320.539
1330.265
1340.388
1350.0424
1360.00552
1370.462
1380.396
1390.346
140.714
1400.614
1410.208
1420.763
1430.0578
1440.0104
1450.0132
1460.309
1470.566
1480.28
1490.208
150.41
1500.475
1510.584
1520.464
1530.815
1540.589
1550.948
1560.39
1570.441
1580.309
1590.745
1600.879
1610.689
1620.113
1630.682
1640.189
1650.188
1660.529
1670.214
1680.92
1690.235
170.187
180.179
190.628
20.206
200.0743
210.795
220.931
230.31
240.146
250.153
260.00235
270.828
280.894
290.00681
30.483
300.826
310.324
320.263
330.075
340.437
350.815
360.15
370.322
380.696
390.656
40.457
400.0536
410.254
420.85
430.648
440.88
450.86
460.409
470.705
480.336
490.844
50.76
500.864
510.825
520.732
530.414
540.959
550.935
560.967
570.706
580.293
590.648
60.64
600.179
610.279
620.286
630.555
640.735
650.839
660.324
670.559
680.761
690.143
70.0196
700.258
710.0363
720.464
730.0544
740.697
750.0164
760.57
770.772
780.0489
790.961
80.358
800.674
810.425
820.643
830.438
840.668
850.952
860.369
870.00396
880.5
890.978
90.708
900.164
910.0199
920.0898
930.111
940.427
958.47968e-4
960.456
970.939
980.634
990.753



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: CNhs12557


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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