FF:10101-102D2

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 strain C57BL/6J tissue whole body dev stage 17.5 days embryo sex NA age NA cell type CELL MIXTURE - tissue sample cell line NA company NA collaboration FANTOM5 OSC CORE (contact: Al Forrest) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type total RNA extraction protocol (Details) 1

Accession numbers

Method Sample accession id CAGE  SAMD00021108 Library accession numbers Library id Method Exp. accession id Run accession id CNhs13047 CAGE DRX023634 DRR026029 CNhs13071 CAGE DRX023635 DRR026030 CNhs13198 CAGE DRX023636 DRR026031 CNhs13222 CAGE DRX023637 DRR026032 CNhs13438 CAGE DRX023638 DRR026033 CNhs13462 CAGE DRX023639 DRR026034 CNhs13486 CAGE DRX023640 DRR026035 CNhs13510 CAGE DRX023641 DRR026036 CNhs13534 CAGE DRX023642 DRR026037 CNhs13558 CAGE DRX023643 DRR026038 CNhs12613 CAGE DRX023672 DRR026067 CNhs12637 CAGE DRX023673 DRR026068 CNhs12661 CAGE DRX023674 DRR026069 CNhs12685 CAGE DRX023675 DRR026070 CNhs12729 CAGE DRX023676 DRR026071 CNhs12841 CAGE DRX023677 DRR026072 CNhs12865 CAGE DRX023678 DRR026073 CNhs12959 CAGE DRX023679 DRR026074 CNhs12999 CAGE DRX023680 DRR026075 CNhs13023 CAGE DRX023681 DRR026076 CNhs12457 CAGE DRX023686 DRR026081 CNhs12481 CAGE DRX023687 DRR026082 CNhs12793 CAGE DRX023688 DRR026083 CNhs12817 CAGE DRX023689 DRR026084 CNhs12745 CAGE DRX023690 DRR026085 CNhs12769 CAGE DRX023691 DRR026086 CNhs13246 CAGE DRX023692 DRR026087 CNhs13270 CAGE DRX023693 DRR026088 CNhs12889 CAGE DRX023694 DRR026089 CNhs12913 CAGE DRX023695 DRR026090 CNhs13095 CAGE DRX023696 DRR026091 CNhs13119 CAGE DRX023697 DRR026092 CNhs13143 CAGE DRX023698 DRR026093 CNhs13167 CAGE DRX023699 DRR026094 CNhs13294 CAGE DRX023700 DRR026095 CNhs13318 CAGE DRX023701 DRR026096 CNhs13342 CAGE DRX023702 DRR026097 CNhs13366 CAGE DRX023703 DRR026098 CNhs13390 CAGE DRX023704 DRR026099 CNhs13414 CAGE DRX023705 DRR026100 CNhs13618 CAGE DRX023706 DRR026101 CNhs13642 CAGE DRX023707 DRR026102 CNhs12983 CAGE DRX023708 DRR026103 CNhs13713 CAGE DRX023709 DRR026104 CNhs13737 CAGE DRX023710 DRR026105 CNhs13761 CAGE DRX023711 DRR026106 CNhs13785 CAGE DRX023712 DRR026107 CNhs13810 CAGE DRX023715 DRR026110 CNhs13834 CAGE DRX023716 DRR026111 CNhs13570 CAGE DRX023723 DRR026118 CNhs13594 CAGE DRX023724 DRR026119 CNhs12409 CAGE DRX023725 DRR026121 DRR026122 DRR026120 DRR026121 DRR026122 CNhs12433 CAGE DRX023726 DRR026124 DRR026125 DRR026123 DRR026124 DRR026125 CNhs13685 CAGE DRX023729 DRR026128 CNhs13923 CAGE DRX023730 DRR026129 CNhs14372 CAGE DRX023746 DRR026145 CNhs14373 CAGE DRX023747 DRR026146 CNhs13230 CAGE DRX023749 DRR026148 CNhs12521 CAGE DRX023750 DRR026149 CNhs12537 CAGE DRX023751 DRR026150 CNhs12561 CAGE DRX023752 DRR026151 Accession ID Mm9 Library id BAM CTSS CNhs13047 DRZ005281 DRZ006071 CNhs13071 DRZ005282 DRZ006072 CNhs13198 DRZ005283 DRZ006073 CNhs13222 DRZ005284 DRZ006074 CNhs13438 DRZ005285 DRZ006075 CNhs13462 DRZ005286 DRZ006076 CNhs13486 DRZ005287 DRZ006077 CNhs13510 DRZ005288 DRZ006078 CNhs13534 DRZ005289 DRZ006079 CNhs13558 DRZ005290 DRZ006080 CNhs12613 DRZ005319 DRZ006109 CNhs12637 DRZ005320 DRZ006110 CNhs12661 DRZ005321 DRZ006111 CNhs12685 DRZ005322 DRZ006112 CNhs12729 DRZ005323 DRZ006113 CNhs12841 DRZ005324 DRZ006114 CNhs12865 DRZ005325 DRZ006115 CNhs12959 DRZ005326 DRZ006116 CNhs12999 DRZ005327 DRZ006117 CNhs13023 DRZ005328 DRZ006118 CNhs12457 DRZ005333 DRZ006123 CNhs12481 DRZ005334 DRZ006124 CNhs12793 DRZ005335 DRZ006125 CNhs12817 DRZ005336 DRZ006126 CNhs12745 DRZ005337 DRZ006127 CNhs12769 DRZ005338 DRZ006128 CNhs13246 DRZ005339 DRZ006129 CNhs13270 DRZ005340 DRZ006130 CNhs12889 DRZ005341 DRZ006131 CNhs12913 DRZ005342 DRZ006132 CNhs13095 DRZ005343 DRZ006133 CNhs13119 DRZ005344 DRZ006134 CNhs13143 DRZ005345 DRZ006135 CNhs13167 DRZ005346 DRZ006136 CNhs13294 DRZ005347 DRZ006137 CNhs13318 DRZ005348 DRZ006138 CNhs13342 DRZ005349 DRZ006139 CNhs13366 DRZ005350 DRZ006140 CNhs13390 DRZ005351 DRZ006141 CNhs13414 DRZ005352 DRZ006142 CNhs13618 DRZ005353 DRZ006143 CNhs13642 DRZ005354 DRZ006144 CNhs12983 DRZ005355 DRZ006145 CNhs13713 DRZ005356 DRZ006146 CNhs13737 DRZ005357 DRZ006147 CNhs13761 DRZ005358 DRZ006148 CNhs13785 DRZ005359 DRZ006149 CNhs13810 DRZ005362 DRZ006152 CNhs13834 DRZ005363 DRZ006153 CNhs13570 DRZ005370 DRZ006160 CNhs13594 DRZ005371 DRZ006161 CNhs12409 DRZ005372 DRZ005373 DRZ005374 DRZ006162 CNhs12433 DRZ005375 DRZ005376 DRZ005377 DRZ006163 CNhs13685 DRZ005380 DRZ006166 CNhs13923 DRZ005381 DRZ006167 CNhs14372 DRZ005397 DRZ006183 CNhs14373 DRZ005398 DRZ006184 CNhs13230 DRZ005400 DRZ006186 CNhs12521 DRZ005401 DRZ006187 CNhs12537 DRZ005402 DRZ006188 CNhs12561 DRZ005403 DRZ006189 Accession ID Mm10 Library id BAM CTSS 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

Download raw sequence, BAM & CTSS
Mm9 Fasta BAM CTSS download download donwload Mm10 BAM CTSS download 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.
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 no result for this sample

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

is_a relathionship
EFO:0001461 control
FF:0011374 mouse whole body- embryo E17.5 sample

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)