FF:10101-102D3

Name:	whole body, embryo E17.5, pool1 (internal control)
Species:	Mouse (Mus musculus)
Library ID:	CNhs13928,CNhs13929,CNhs13930,CNhs13931,CNhs13932,CNhs13933,CNhs13934,CNhs13935,CNhs13967
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

CAGE Accession numbers

Method Sample accession id CAGE  SAMD00021109 Library accession numbers Library id Method Exp. accession id Run accession id CNhs13928 CAGE DRX023717 DRR026112 CNhs13929 CAGE DRX023718 DRR026113 CNhs13930 CAGE DRX023719 DRR026114 CNhs13931 CAGE DRX023720 DRR026115 CNhs13932 CAGE DRX023721 DRR026116 CNhs13933 CAGE DRX023722 DRR026117 CNhs13934 CAGE DRX023736 DRR026135 CNhs13935 CAGE DRX023737 DRR026136 CNhs13967 CAGE DRX023739 DRR026138 Accession ID Mm9 Library id BAM CTSS CNhs13928 DRZ005364 DRZ006154 CNhs13929 DRZ005365 DRZ006155 CNhs13930 DRZ005366 DRZ006156 CNhs13931 DRZ005367 DRZ006157 CNhs13932 DRZ005368 DRZ006158 CNhs13933 DRZ005369 DRZ006159 CNhs13934 DRZ005387 DRZ006173 CNhs13935 DRZ005388 DRZ006174 CNhs13967 DRZ005390 DRZ006176 Accession ID Mm10 Library id BAM CTSS CNhs13928 CNhs13929 CNhs13930 CNhs13931 CNhs13932 CNhs13933 CNhs13934 CNhs13935 CNhs13967

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

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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)