FF:3139-67G5

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 strain C57BL/6J tissue whole body dev stage 17.5 days embryo sex unknown_sex_type 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 NA extraction protocol (Details) NA

CAGE Accession numbers

Method Sample accession id CAGE  SAMD00005832 Library accession numbers Library id Method Exp. accession id Run accession id CNhs10479 CAGE DRX008871 DRR009743 CNhs10495 CAGE DRX008872 DRR009744 CNhs10511 CAGE DRX008873 DRR009745 CNhs10527 CAGE DRX008874 DRR009746 CNhs10591 CAGE DRX008875 DRR009747 CNhs10607 CAGE DRX008876 DRR009748 CNhs10623 CAGE DRX008877 DRR009749 CNhs10639 CAGE DRX008878 DRR009750 CNhs10655 CAGE DRX008879 DRR009751 CNhs10725 CAGE DRX008880 DRR009752 CNhs10749 CAGE DRX008881 DRR009753 CNhs10840 CAGE DRX008882 DRR009754 CNhs10856 CAGE DRX008883 DRR009755 CNhs10880 CAGE DRX008884 DRR009756 CNhs11000 CAGE DRX008885 DRR009757 CNhs11024 CAGE DRX008886 DRR009758 CNhs11032 CAGE DRX008887 DRR009759 CNhs11048 CAGE DRX008888 DRR009760 CNhs11072 CAGE DRX008889 DRR009761 CNhs11080 CAGE DRX008890 DRR009762 CNhs11096 CAGE DRX008891 DRR009763 CNhs11120 CAGE DRX008892 DRR009764 CNhs11128 CAGE DRX008893 DRR009765 CNhs11184 CAGE DRX008894 DRR009766 CNhs11208 CAGE DRX008895 DRR009767 CNhs11216 CAGE DRX008896 DRR009768 CNhs11246 CAGE DRX008897 DRR009769 CNhs11278 CAGE DRX008898 DRR009770 CNhs11318 CAGE DRX023644 DRR026039 CNhs11374 CAGE DRX023645 DRR026040 CNhs11668 CAGE DRX023646 DRR026041 CNhs11706 CAGE DRX023647 DRR026042 CNhs11730 CAGE DRX023648 DRR026043 CNhs11754 CAGE DRX023649 DRR026044 CNhs11778 CAGE DRX023650 DRR026045 CNhs11802 CAGE DRX023651 DRR026046 CNhs11826 CAGE DRX023652 DRR026047 CNhs11850 CAGE DRX023653 DRR026048 CNhs11874 CAGE DRX023654 DRR026049 CNhs11898 CAGE DRX023655 DRR026050 CNhs11938 CAGE DRX023656 DRR026051 CNhs11946 CAGE DRX023657 DRR026052 CNhs11970 CAGE DRX023658 DRR026053 CNhs11994 CAGE DRX023659 DRR026054 CNhs12018 CAGE DRX023660 DRR026055 CNhs12042 CAGE DRX023661 DRR026056 CNhs12066 CAGE DRX023662 DRR026057 CNhs12090 CAGE DRX023663 DRR026058 CNhs12114 CAGE DRX023664 DRR026059 CNhs12230 CAGE DRX023665 DRR026060 CNhs11262 CAGE DRX023666 DRR026061 CNhs11294 CAGE DRX023667 DRR026062 CNhs12361 CAGE DRX023668 DRR026063 CNhs12385 CAGE DRX023669 DRR026064 CNhs12577 CAGE DRX023670 DRR026065 CNhs12505 CAGE DRX023671 DRR026066 CNhs11916 CAGE DRX023682 DRR026077 CNhs12585 CAGE DRX023683 DRR026078 CNhs12313 CAGE DRX023684 DRR026079 CNhs12337 CAGE DRX023685 DRR026080 CNhs11326 CAGE DRX023713 DRR026108 CNhs11342 CAGE DRX023714 DRR026109 CNhs12186 CAGE DRX023753 DRR026152 CNhs12194 CAGE DRX023754 DRR026153 Accession ID Mm9 Library id BAM CTSS CNhs10479 DRZ001168 DRZ002553 CNhs10495 DRZ001169 DRZ002554 CNhs10511 DRZ001170 DRZ002555 CNhs10527 DRZ001171 DRZ002556 CNhs10591 DRZ001172 DRZ002557 CNhs10607 DRZ001173 DRZ002558 CNhs10623 DRZ001174 DRZ002559 CNhs10639 DRZ001175 DRZ002560 CNhs10655 DRZ001176 DRZ002561 CNhs10725 DRZ001177 DRZ002562 CNhs10749 DRZ001178 DRZ002563 CNhs10840 DRZ001179 DRZ002564 CNhs10856 DRZ001180 DRZ002565 CNhs10880 DRZ001181 DRZ002566 CNhs11000 DRZ001182 DRZ002567 CNhs11024 DRZ001183 DRZ002568 CNhs11032 DRZ001184 DRZ002569 CNhs11048 DRZ001185 DRZ002570 CNhs11072 DRZ001186 DRZ002571 CNhs11080 DRZ001187 DRZ002572 CNhs11096 DRZ001188 DRZ002573 CNhs11120 DRZ001189 DRZ002574 CNhs11128 DRZ001190 DRZ002575 CNhs11184 DRZ001191 DRZ002576 CNhs11208 DRZ001192 DRZ002577 CNhs11216 DRZ001193 DRZ002578 CNhs11246 DRZ001194 DRZ002579 CNhs11278 DRZ001195 DRZ002580 CNhs11318 DRZ005291 DRZ006081 CNhs11374 DRZ005292 DRZ006082 CNhs11668 DRZ005293 DRZ006083 CNhs11706 DRZ005294 DRZ006084 CNhs11730 DRZ005295 DRZ006085 CNhs11754 DRZ005296 DRZ006086 CNhs11778 DRZ005297 DRZ006087 CNhs11802 DRZ005298 DRZ006088 CNhs11826 DRZ005299 DRZ006089 CNhs11850 DRZ005300 DRZ006090 CNhs11874 DRZ005301 DRZ006091 CNhs11898 DRZ005302 DRZ006092 CNhs11938 DRZ005303 DRZ006093 CNhs11946 DRZ005304 DRZ006094 CNhs11970 DRZ005305 DRZ006095 CNhs11994 DRZ005306 DRZ006096 CNhs12018 DRZ005307 DRZ006097 CNhs12042 DRZ005308 DRZ006098 CNhs12066 DRZ005309 DRZ006099 CNhs12090 DRZ005310 DRZ006100 CNhs12114 DRZ005311 DRZ006101 CNhs12230 DRZ005312 DRZ006102 CNhs11262 DRZ005313 DRZ006103 CNhs11294 DRZ005314 DRZ006104 CNhs12361 DRZ005315 DRZ006105 CNhs12385 DRZ005316 DRZ006106 CNhs12577 DRZ005317 DRZ006107 CNhs12505 DRZ005318 DRZ006108 CNhs11916 DRZ005329 DRZ006119 CNhs12585 DRZ005330 DRZ006120 CNhs12313 DRZ005331 DRZ006121 CNhs12337 DRZ005332 DRZ006122 CNhs11326 DRZ005360 DRZ006150 CNhs11342 DRZ005361 DRZ006151 CNhs12186 DRZ005404 DRZ006190 CNhs12194 DRZ005405 DRZ006191 Accession ID Mm10 Library id BAM CTSS CNhs10479 DRZ012518 DRZ013903 CNhs10495 DRZ012519 DRZ013904 CNhs10511 DRZ012520 DRZ013905 CNhs10527 DRZ012521 DRZ013906 CNhs10591 DRZ012522 DRZ013907 CNhs10607 DRZ012523 DRZ013908 CNhs10623 DRZ012524 DRZ013909 CNhs10639 DRZ012525 DRZ013910 CNhs10655 DRZ012526 DRZ013911 CNhs10725 DRZ012527 DRZ013912 CNhs10749 DRZ012528 DRZ013913 CNhs10840 DRZ012529 DRZ013914 CNhs10856 DRZ012530 DRZ013915 CNhs10880 DRZ012531 DRZ013916 CNhs11000 DRZ012532 DRZ013917 CNhs11024 DRZ012533 DRZ013918 CNhs11032 DRZ012534 DRZ013919 CNhs11048 DRZ012535 DRZ013920 CNhs11072 DRZ012536 DRZ013921 CNhs11080 DRZ012537 DRZ013922 CNhs11096 DRZ012538 DRZ013923 CNhs11120 DRZ012539 DRZ013924 CNhs11128 DRZ012540 DRZ013925 CNhs11184 DRZ012541 DRZ013926 CNhs11208 DRZ012542 DRZ013927 CNhs11216 DRZ012543 DRZ013928 CNhs11246 DRZ012544 DRZ013929 CNhs11278 DRZ012545 DRZ013930 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

Download raw sequence, BAM & CTSS
Mm9 Fasta BAM CTSS download download donwload Mm10 BAM CTSS download donwload

Relative expression to median (log10)

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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. <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

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

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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

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Direct parent terms

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

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)