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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021108
|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=
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|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|expression_enrichment_score=
|expression_enrichment_score=
|ffid_belonging_in_development=FF:0000294
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|id=
|id=FF:10101-102D2
|is_a=EFO:0001461;;FF:0011374
|is_a=EFO:0001461;;FF:0011374
|is_obsolete=
|is_obsolete=
|name=
|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
|library_id_phase_based=2: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
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.qualitycontrol.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs13023.10101-102D2.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.qualitycontrol.hCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs13023.10101-102D2.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.qualitycontrol.LQhCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs12561.10101-102D2.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.qualitycontrol.LQhCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs12561.10101-102D2.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.qualitycontrol.LQhCAGE/whole%2520body%252c%2520embryo%2520E17%252e5%252c%2520pool1%2520%2528internal%2520control%2529.CNhs12561.10101-102D2.mm9.nobarcode.rdna.fa.gz
|name=whole body, embryo E17.5, pool1 (internal control)
|namespace=
|namespace=
|part_of=
|part_of=
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|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=
|profile_srnaseq=
|rna_box=
|rna_box=102
|rna_catalog_number=
|rna_catalog_number=NA
|rna_concentration=
|rna_concentration=159
|rna_extraction_protocol=
|rna_extraction_protocol=1
|rna_lot_number=
|rna_lot_number=NA
|rna_od260/230=
|rna_od260/230=2.1
|rna_od260/280=
|rna_od260/280=2
|rna_position=
|rna_position=D4
|rna_rin=
|rna_rin=8.5
|rna_sample_type=
|rna_sample_type=total RNA
|rna_tube_id=
|rna_tube_id=102D4
|rna_weight_ug=
|rna_weight_ug=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|sample_age=
|sample_age=
|sample_cell_catalog=
|sample_category=control
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_lot=NA
|sample_cell_type=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=
|sample_company=NA
|sample_description=
|sample_description=
|sample_dev_stage=
|sample_dev_stage=17.5 days embryo
|sample_disease=
|sample_disease=normal
|sample_donor(cell lot)=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_ethnicity=
|sample_experimental_condition=
|sample_experimental_condition=
|sample_id=
|sample_id=10101
|sample_note=
|sample_note=
|sample_sex=
|sample_sex=
|sample_species=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_strain=C57BL/6J
|sample_tissue=
|sample_tissue=whole body
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:10101-102D2;search_select_hide=table117:10101-102D2
}}
}}

Latest revision as of 12:21, 3 June 2020


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
ZENBU report :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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021108
Library accession numbers

Library idMethodExp. accession idRun 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 idBAMCTSS
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
Download raw sequence, BAM & CTSS
Mm9
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Mm10
BAMCTSS
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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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