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
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 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 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 Accession ID Mm10 Library id BAM CTSS 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

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)