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{{f5samples
{{f5samples
|accession_numbers=CAGE;DRX023634;DRR026029;DRZ005281;DRZ006071!CAGE;DRX023635;DRR026030;DRZ005282;DRZ006072!CAGE;DRX023636;DRR026031;DRZ005283;DRZ006073!CAGE;DRX023637;DRR026032;DRZ005284;DRZ006074!CAGE;DRX023638;DRR026033;DRZ005285;DRZ006075!CAGE;DRX023639;DRR026034;DRZ005286;DRZ006076!CAGE;DRX023640;DRR026035;DRZ005287;DRZ006077!CAGE;DRX023641;DRR026036;DRZ005288;DRZ006078!CAGE;DRX023642;DRR026037;DRZ005289;DRZ006079!CAGE;DRX023643;DRR026038;DRZ005290;DRZ006080!CAGE;DRX023672;DRR026067;DRZ005319;DRZ006109!CAGE;DRX023673;DRR026068;DRZ005320;DRZ006110!CAGE;DRX023674;DRR026069;DRZ005321;DRZ006111!CAGE;DRX023675;DRR026070;DRZ005322;DRZ006112!CAGE;DRX023676;DRR026071;DRZ005323;DRZ006113!CAGE;DRX023677;DRR026072;DRZ005324;DRZ006114!CAGE;DRX023678;DRR026073;DRZ005325;DRZ006115!CAGE;DRX023679;DRR026074;DRZ005326;DRZ006116!CAGE;DRX023680;DRR026075;DRZ005327;DRZ006117!CAGE;DRX023681;DRR026076;DRZ005328;DRZ006118!CAGE;DRX023686;DRR026081;DRZ005333;DRZ006123!CAGE;DRX023687;DRR026082;DRZ005334;DRZ006124!CAGE;DRX023688;DRR026083;DRZ005335;DRZ006125!CAGE;DRX023689;DRR026084;DRZ005336;DRZ006126!CAGE;DRX023690;DRR026085;DRZ005337;DRZ006127!CAGE;DRX023691;DRR026086;DRZ005338;DRZ006128!CAGE;DRX023692;DRR026087;DRZ005339;DRZ006129!CAGE;DRX023693;DRR026088;DRZ005340;DRZ006130!CAGE;DRX023694;DRR026089;DRZ005341;DRZ006131!CAGE;DRX023695;DRR026090;DRZ005342;DRZ006132!CAGE;DRX023696;DRR026091;DRZ005343;DRZ006133!CAGE;DRX023697;DRR026092;DRZ005344;DRZ006134!CAGE;DRX023698;DRR026093;DRZ005345;DRZ006135!CAGE;DRX023699;DRR026094;DRZ005346;DRZ006136!CAGE;DRX023700;DRR026095;DRZ005347;DRZ006137!CAGE;DRX023701;DRR026096;DRZ005348;DRZ006138!CAGE;DRX023702;DRR026097;DRZ005349;DRZ006139!CAGE;DRX023703;DRR026098;DRZ005350;DRZ006140!CAGE;DRX023704;DRR026099;DRZ005351;DRZ006141!CAGE;DRX023705;DRR026100;DRZ005352;DRZ006142!CAGE;DRX023706;DRR026101;DRZ005353;DRZ006143!CAGE;DRX023707;DRR026102;DRZ005354;DRZ006144!CAGE;DRX023708;DRR026103;DRZ005355;DRZ006145!CAGE;DRX023709;DRR026104;DRZ005356;DRZ006146!CAGE;DRX023710;DRR026105;DRZ005357;DRZ006147!CAGE;DRX023711;DRR026106;DRZ005358;DRZ006148!CAGE;DRX023712;DRR026107;DRZ005359;DRZ006149!CAGE;DRX023715;DRR026110;DRZ005362;DRZ006152!CAGE;DRX023716;DRR026111;DRZ005363;DRZ006153!CAGE;DRX023723;DRR026118;DRZ005370;DRZ006160!CAGE;DRX023724;DRR026119;DRZ005371;DRZ006161!CAGE;DRX023725;DRR026120 DRR026121 DRR026122;DRZ005372 DRZ005373 DRZ005374;DRZ006162!CAGE;DRX023726;DRR026123 DRR026124 DRR026125;DRZ005375 DRZ005376 DRZ005377;DRZ006163!CAGE;DRX023729;DRR026128;DRZ005380;DRZ006166!CAGE;DRX023730;DRR026129;DRZ005381;DRZ006167!CAGE;DRX023746;DRR026145;DRZ005397;DRZ006183!CAGE;DRX023747;DRR026146;DRZ005398;DRZ006184!CAGE;DRX023749;DRR026148;DRZ005400;DRZ006186!CAGE;DRX023750;DRR026149;DRZ005401;DRZ006187!CAGE;DRX023751;DRR026150;DRZ005402;DRZ006188!CAGE;DRX023752;DRR026151;DRZ005403;DRZ006189
|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 15:18, 2 December 2014


Name:whole body, embryo E17.5, pool1 (internal control)
Species:Mouse (Mus musculus)
Library ID:CNhs13047,CNhs13071,CNhs13198,CNhs13222,CNhs13438,CNhs13462,CNhs13486,CNhs13510,CNhs13534,CNhs13558,CNhs12613,CNhs12637,CNhs12661,CNhs12685,CNhs12729,CNhs12841,CNhs12865,CNhs12959,CNhs12999,CNhs13023,CNhs12457,CNhs12481,CNhs12793,CNhs12817,CNhs12745,CNhs12769,CNhs13246,CNhs13270,CNhs12889,CNhs12913,CNhs13095,CNhs13119,CNhs13143,CNhs13167,CNhs13294,CNhs13318,CNhs13342,CNhs13366,CNhs13390,CNhs13414,CNhs13618,CNhs13642,CNhs12983,CNhs13713,CNhs13737,CNhs13761,CNhs13785,CNhs13810,CNhs13834,CNhs13570,CNhs13594,CNhs12409,CNhs12433,CNhs13685,CNhs13923,CNhs14372,CNhs14373,CNhs13230,CNhs12521,CNhs12537,CNhs12561
Sample type:control
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuewhole body
dev stage17.5 days embryo
sexNA
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 typetotal RNA
extraction protocol (Details)1
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

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



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



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>


FANTOM5 (FF) ontology

Direct parent terms


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

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)<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
FF:0000294 (mouse embryonic day 11 sample)

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