FF:3139-67G5

Name:	whole body, embryo E17.5, pool1 (internal control)
Species:	Mouse (Mus musculus)
Library ID:	{{{library_id}}}
Sample type:	developmental
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  DRS008761 Library accession numbers Library id Method Exp. accession id Run accession id {{{library_id}}} CAGE DRX008871 DRR009743 CAGE DRX008872 DRR009744 CAGE DRX008873 DRR009745 CAGE DRX008874 DRR009746 CAGE DRX008875 DRR009747 CAGE DRX008876 DRR009748 CAGE DRX008877 DRR009749 CAGE DRX008878 DRR009750 CAGE DRX008879 DRR009751 CAGE DRX008880 DRR009752 CAGE DRX008881 DRR009753 CAGE DRX008882 DRR009754 CAGE DRX008883 DRR009755 CAGE DRX008884 DRR009756 CAGE DRX008885 DRR009757 CAGE DRX008886 DRR009758 CAGE DRX008887 DRR009759 CAGE DRX008888 DRR009760 CAGE DRX008889 DRR009761 CAGE DRX008890 DRR009762 CAGE DRX008891 DRR009763 CAGE DRX008892 DRR009764 CAGE DRX008893 DRR009765 CAGE DRX008894 DRR009766 CAGE DRX008895 DRR009767 CAGE DRX008896 DRR009768 CAGE DRX008897 DRR009769 CAGE DRX008898 DRR009770 Accession ID Mm9 Library id BAM CTSS {{{library_id}}} DRZ001168 DRZ002553 DRZ001169 DRZ002554 DRZ001170 DRZ002555 DRZ001171 DRZ002556 DRZ001172 DRZ002557 DRZ001173 DRZ002558 DRZ001174 DRZ002559 DRZ001175 DRZ002560 DRZ001176 DRZ002561 DRZ001177 DRZ002562 DRZ001178 DRZ002563 DRZ001179 DRZ002564 DRZ001180 DRZ002565 DRZ001181 DRZ002566 DRZ001182 DRZ002567 DRZ001183 DRZ002568 DRZ001184 DRZ002569 DRZ001185 DRZ002570 DRZ001186 DRZ002571 DRZ001187 DRZ002572 DRZ001188 DRZ002573 DRZ001189 DRZ002574 DRZ001190 DRZ002575 DRZ001191 DRZ002576 DRZ001192 DRZ002577 DRZ001193 DRZ002578 DRZ001194 DRZ002579 DRZ001195 DRZ002580 Accession ID Mm10 Library id BAM CTSS {{{library_id}}}

Download raw sequence, BAM & CTSS
Mm9 BAM CTSS [{{{mm9bam}}} download] [{{{mm9ctss}}} donwload] Mm10 BAM CTSS [{{{mm10bam}}} download] [{{{mm10ctss}}} 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

multiple

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
library id: multipleThis sample isn't target for the analysis

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
library id: multipleThis sample isn't target for the analysis

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> library id: multiple

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)