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{{f5samples
 
{{f5samples
 
|DRA_sample_Accession=CAGE@SAMD00005832
 
|DRA_sample_Accession=CAGE@SAMD00005832
|accession_numbers=CAGE;DRX008871;DRR009743;DRZ001168;DRZ002553!CAGE;DRX008872;DRR009744;DRZ001169;DRZ002554!CAGE;DRX008873;DRR009745;DRZ001170;DRZ002555!CAGE;DRX008874;DRR009746;DRZ001171;DRZ002556!CAGE;DRX008875;DRR009747;DRZ001172;DRZ002557!CAGE;DRX008876;DRR009748;DRZ001173;DRZ002558!CAGE;DRX008877;DRR009749;DRZ001174;DRZ002559!CAGE;DRX008878;DRR009750;DRZ001175;DRZ002560!CAGE;DRX008879;DRR009751;DRZ001176;DRZ002561!CAGE;DRX008880;DRR009752;DRZ001177;DRZ002562!CAGE;DRX008881;DRR009753;DRZ001178;DRZ002563!CAGE;DRX008882;DRR009754;DRZ001179;DRZ002564!CAGE;DRX008883;DRR009755;DRZ001180;DRZ002565!CAGE;DRX008884;DRR009756;DRZ001181;DRZ002566!CAGE;DRX008885;DRR009757;DRZ001182;DRZ002567!CAGE;DRX008886;DRR009758;DRZ001183;DRZ002568!CAGE;DRX008887;DRR009759;DRZ001184;DRZ002569!CAGE;DRX008888;DRR009760;DRZ001185;DRZ002570!CAGE;DRX008889;DRR009761;DRZ001186;DRZ002571!CAGE;DRX008890;DRR009762;DRZ001187;DRZ002572!CAGE;DRX008891;DRR009763;DRZ001188;DRZ002573!CAGE;DRX008892;DRR009764;DRZ001189;DRZ002574!CAGE;DRX008893;DRR009765;DRZ001190;DRZ002575!CAGE;DRX008894;DRR009766;DRZ001191;DRZ002576!CAGE;DRX008895;DRR009767;DRZ001192;DRZ002577!CAGE;DRX008896;DRR009768;DRZ001193;DRZ002578!CAGE;DRX008897;DRR009769;DRZ001194;DRZ002579!CAGE;DRX008898;DRR009770;DRZ001195;DRZ002580
+
|accession_numbers=CAGE;DRX008872;DRR009744;DRZ001169;DRZ002554!CAGE;DRX008873;DRR009745;DRZ001170;DRZ002555!CAGE;DRX008874;DRR009746;DRZ001171;DRZ002556!CAGE;DRX008875;DRR009747;DRZ001172;DRZ002557!CAGE;DRX008876;DRR009748;DRZ001173;DRZ002558!CAGE;DRX008877;DRR009749;DRZ001174;DRZ002559!CAGE;DRX008878;DRR009750;DRZ001175;DRZ002560!CAGE;DRX008879;DRR009751;DRZ001176;DRZ002561!CAGE;DRX008880;DRR009752;DRZ001177;DRZ002562!CAGE;DRX008881;DRR009753;DRZ001178;DRZ002563!CAGE;DRX008882;DRR009754;DRZ001179;DRZ002564!CAGE;DRX008883;DRR009755;DRZ001180;DRZ002565!CAGE;DRX008884;DRR009756;DRZ001181;DRZ002566!CAGE;DRX008885;DRR009757;DRZ001182;DRZ002567!CAGE;DRX008886;DRR009758;DRZ001183;DRZ002568!CAGE;DRX008887;DRR009759;DRZ001184;DRZ002569!CAGE;DRX008888;DRR009760;DRZ001185;DRZ002570!CAGE;DRX008889;DRR009761;DRZ001186;DRZ002571!CAGE;DRX008890;DRR009762;DRZ001187;DRZ002572!CAGE;DRX008891;DRR009763;DRZ001188;DRZ002573!CAGE;DRX008892;DRR009764;DRZ001189;DRZ002574!CAGE;DRX008893;DRR009765;DRZ001190;DRZ002575!CAGE;DRX008894;DRR009766;DRZ001191;DRZ002576!CAGE;DRX008895;DRR009767;DRZ001192;DRZ002577!CAGE;DRX008896;DRR009768;DRZ001193;DRZ002578!CAGE;DRX008897;DRR009769;DRZ001194;DRZ002579!CAGE;DRX008898;DRR009770;DRZ001195;DRZ002580!CAGE;DRX023644;DRR026039;DRZ005291;DRZ006081!CAGE;DRX023645;DRR026040;DRZ005292;DRZ006082!CAGE;DRX023646;DRR026041;DRZ005293;DRZ006083!CAGE;DRX023647;DRR026042;DRZ005294;DRZ006084!CAGE;DRX023648;DRR026043;DRZ005295;DRZ006085!CAGE;DRX023649;DRR026044;DRZ005296;DRZ006086!CAGE;DRX023650;DRR026045;DRZ005297;DRZ006087!CAGE;DRX023651;DRR026046;DRZ005298;DRZ006088!CAGE;DRX023652;DRR026047;DRZ005299;DRZ006089!CAGE;DRX023653;DRR026048;DRZ005300;DRZ006090!CAGE;DRX023654;DRR026049;DRZ005301;DRZ006091!CAGE;DRX023655;DRR026050;DRZ005302;DRZ006092!CAGE;DRX023656;DRR026051;DRZ005303;DRZ006093!CAGE;DRX023657;DRR026052;DRZ005304;DRZ006094!CAGE;DRX023658;DRR026053;DRZ005305;DRZ006095!CAGE;DRX023659;DRR026054;DRZ005306;DRZ006096!CAGE;DRX023660;DRR026055;DRZ005307;DRZ006097!CAGE;DRX023661;DRR026056;DRZ005308;DRZ006098!CAGE;DRX023662;DRR026057;DRZ005309;DRZ006099!CAGE;DRX023663;DRR026058;DRZ005310;DRZ006100!CAGE;DRX023664;DRR026059;DRZ005311;DRZ006101!CAGE;DRX023665;DRR026060;DRZ005312;DRZ006102!CAGE;DRX023666;DRR026061;DRZ005313;DRZ006103!CAGE;DRX023667;DRR026062;DRZ005314;DRZ006104!CAGE;DRX023668;DRR026063;DRZ005315;DRZ006105!CAGE;DRX023669;DRR026064;DRZ005316;DRZ006106!CAGE;DRX023670;DRR026065;DRZ005317;DRZ006107!CAGE;DRX023671;DRR026066;DRZ005318;DRZ006108!CAGE;DRX023682;DRR026077;DRZ005329;DRZ006119!CAGE;DRX023683;DRR026078;DRZ005330;DRZ006120!CAGE;DRX023684;DRR026079;DRZ005331;DRZ006121!CAGE;DRX023685;DRR026080;DRZ005332;DRZ006122!CAGE;DRX023713;DRR026108;DRZ005360;DRZ006150!CAGE;DRX023714;DRR026109;DRZ005361;DRZ006151!CAGE;DRX023753;DRR026152;DRZ005404;DRZ006190!CAGE;DRX023754;DRR026153;DRZ005405;DRZ006191
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
 
|ancestors_in_cell_lineage_facet=
 
|ancestors_in_cell_lineage_facet=

Revision as of 05:26, 2 December 2014


Name:whole body, embryo E17.5, pool1 (internal control)
Species:Mouse (Mus musculus)
Library ID:CNhs10479,CNhs10495,CNhs10511,CNhs10527,CNhs10591,CNhs10607,CNhs10623,CNhs10639,CNhs10655,CNhs10725,CNhs10749,CNhs10840,CNhs10856,CNhs10880,CNhs11000,CNhs11024,CNhs11032,CNhs11048,CNhs11072,CNhs11080,CNhs11096,CNhs11120,CNhs11128,CNhs11184,CNhs11208,CNhs11216,CNhs11246,CNhs11278,CNhs11318,CNhs11374,CNhs11668,CNhs11706,CNhs11730,CNhs11754,CNhs11778,CNhs11802,CNhs11826,CNhs11850,CNhs11874,CNhs11898,CNhs11938,CNhs11946,CNhs11970,CNhs11994,CNhs12018,CNhs12042,CNhs12066,CNhs12090,CNhs12114,CNhs12230,CNhs11262,CNhs11294,CNhs12361,CNhs12385,CNhs12577,CNhs12505,CNhs11916,CNhs12585,CNhs12313,CNhs12337,CNhs11326,CNhs11342,CNhs12186,CNhs12194
Sample type:control
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage17.5 days embryo
sexunknown_sex_type
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

Accession numbers
MethodSample accession id
CAGE  SAMD00005832
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs10479 CAGE DRX008872 DRR009744
CNhs10495 CAGE DRX008873 DRR009745
CNhs10511 CAGE DRX008874 DRR009746
CNhs10527 CAGE DRX008875 DRR009747
CNhs10591 CAGE DRX008876 DRR009748
CNhs10607 CAGE DRX008877 DRR009749
CNhs10623 CAGE DRX008878 DRR009750
CNhs10639 CAGE DRX008879 DRR009751
CNhs10655 CAGE DRX008880 DRR009752
CNhs10725 CAGE DRX008881 DRR009753
CNhs10749 CAGE DRX008882 DRR009754
CNhs10840 CAGE DRX008883 DRR009755
CNhs10856 CAGE DRX008884 DRR009756
CNhs10880 CAGE DRX008885 DRR009757
CNhs11000 CAGE DRX008886 DRR009758
CNhs11024 CAGE DRX008887 DRR009759
CNhs11032 CAGE DRX008888 DRR009760
CNhs11048 CAGE DRX008889 DRR009761
CNhs11072 CAGE DRX008890 DRR009762
CNhs11080 CAGE DRX008891 DRR009763
CNhs11096 CAGE DRX008892 DRR009764
CNhs11120 CAGE DRX008893 DRR009765
CNhs11128 CAGE DRX008894 DRR009766
CNhs11184 CAGE DRX008895 DRR009767
CNhs11208 CAGE DRX008896 DRR009768
CNhs11216 CAGE DRX008897 DRR009769
CNhs11246 CAGE DRX008898 DRR009770
CNhs11278 CAGE DRX023644 DRR026039
CNhs11318 CAGE DRX023645 DRR026040
CNhs11374 CAGE DRX023646 DRR026041
CNhs11668 CAGE DRX023647 DRR026042
CNhs11706 CAGE DRX023648 DRR026043
CNhs11730 CAGE DRX023649 DRR026044
CNhs11754 CAGE DRX023650 DRR026045
CNhs11778 CAGE DRX023651 DRR026046
CNhs11802 CAGE DRX023652 DRR026047
CNhs11826 CAGE DRX023653 DRR026048
CNhs11850 CAGE DRX023654 DRR026049
CNhs11874 CAGE DRX023655 DRR026050
CNhs11898 CAGE DRX023656 DRR026051
CNhs11938 CAGE DRX023657 DRR026052
CNhs11946 CAGE DRX023658 DRR026053
CNhs11970 CAGE DRX023659 DRR026054
CNhs11994 CAGE DRX023660 DRR026055
CNhs12018 CAGE DRX023661 DRR026056
CNhs12042 CAGE DRX023662 DRR026057
CNhs12066 CAGE DRX023663 DRR026058
CNhs12090 CAGE DRX023664 DRR026059
CNhs12114 CAGE DRX023665 DRR026060
CNhs12230 CAGE DRX023666 DRR026061
CNhs11262 CAGE DRX023667 DRR026062
CNhs11294 CAGE DRX023668 DRR026063
CNhs12361 CAGE DRX023669 DRR026064
CNhs12385 CAGE DRX023670 DRR026065
CNhs12577 CAGE DRX023671 DRR026066
CNhs12505 CAGE DRX023682 DRR026077
CNhs11916 CAGE DRX023683 DRR026078
CNhs12585 CAGE DRX023684 DRR026079
CNhs12313 CAGE DRX023685 DRR026080
CNhs12337 CAGE DRX023713 DRR026108
CNhs11326 CAGE DRX023714 DRR026109
CNhs11342 CAGE DRX023753 DRR026152
CNhs12186 CAGE DRX023754 DRR026153
Accession ID Mm9

Library idBAMCTSS
CNhs10479 DRZ001169 DRZ002554
CNhs10495 DRZ001170 DRZ002555
CNhs10511 DRZ001171 DRZ002556
CNhs10527 DRZ001172 DRZ002557
CNhs10591 DRZ001173 DRZ002558
CNhs10607 DRZ001174 DRZ002559
CNhs10623 DRZ001175 DRZ002560
CNhs10639 DRZ001176 DRZ002561
CNhs10655 DRZ001177 DRZ002562
CNhs10725 DRZ001178 DRZ002563
CNhs10749 DRZ001179 DRZ002564
CNhs10840 DRZ001180 DRZ002565
CNhs10856 DRZ001181 DRZ002566
CNhs10880 DRZ001182 DRZ002567
CNhs11000 DRZ001183 DRZ002568
CNhs11024 DRZ001184 DRZ002569
CNhs11032 DRZ001185 DRZ002570
CNhs11048 DRZ001186 DRZ002571
CNhs11072 DRZ001187 DRZ002572
CNhs11080 DRZ001188 DRZ002573
CNhs11096 DRZ001189 DRZ002574
CNhs11120 DRZ001190 DRZ002575
CNhs11128 DRZ001191 DRZ002576
CNhs11184 DRZ001192 DRZ002577
CNhs11208 DRZ001193 DRZ002578
CNhs11216 DRZ001194 DRZ002579
CNhs11246 DRZ001195 DRZ002580
CNhs11278 DRZ005291 DRZ006081
CNhs11318 DRZ005292 DRZ006082
CNhs11374 DRZ005293 DRZ006083
CNhs11668 DRZ005294 DRZ006084
CNhs11706 DRZ005295 DRZ006085
CNhs11730 DRZ005296 DRZ006086
CNhs11754 DRZ005297 DRZ006087
CNhs11778 DRZ005298 DRZ006088
CNhs11802 DRZ005299 DRZ006089
CNhs11826 DRZ005300 DRZ006090
CNhs11850 DRZ005301 DRZ006091
CNhs11874 DRZ005302 DRZ006092
CNhs11898 DRZ005303 DRZ006093
CNhs11938 DRZ005304 DRZ006094
CNhs11946 DRZ005305 DRZ006095
CNhs11970 DRZ005306 DRZ006096
CNhs11994 DRZ005307 DRZ006097
CNhs12018 DRZ005308 DRZ006098
CNhs12042 DRZ005309 DRZ006099
CNhs12066 DRZ005310 DRZ006100
CNhs12090 DRZ005311 DRZ006101
CNhs12114 DRZ005312 DRZ006102
CNhs12230 DRZ005313 DRZ006103
CNhs11262 DRZ005314 DRZ006104
CNhs11294 DRZ005315 DRZ006105
CNhs12361 DRZ005316 DRZ006106
CNhs12385 DRZ005317 DRZ006107
CNhs12577 DRZ005318 DRZ006108
CNhs12505 DRZ005329 DRZ006119
CNhs11916 DRZ005330 DRZ006120
CNhs12585 DRZ005331 DRZ006121
CNhs12313 DRZ005332 DRZ006122
CNhs12337 DRZ005360 DRZ006150
CNhs11326 DRZ005361 DRZ006151
CNhs11342 DRZ005404 DRZ006190
CNhs12186 DRZ005405 DRZ006191
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]


Relative expression to median (log10)


Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



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.
Analyst:NA

link to dataset.
data


Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data



FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data



de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000301 (mouse embryonic day 17.5 sample)
0011374 (mouse whole body- embryo E17.5 sample)

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

FF:0000294 (mouse embryonic day 11 sample)