FF:10101-102D4

Name:	whole body, embryo E17.5, pool1 (internal control)
Species:	Mouse (Mus musculus)
Library ID:	CNhs14096,CNhs14120,CNhs14048,CNhs14072,CNhs14145,CNhs14161,CNhs14185,CNhs14209,CNhs14409,CNhs14433,CNhs14521,CNhs14545,CNhs14569,CNhs14593,CNhs14457,CNhs14377,CNhs14401
Sample type:	control
Genomic View:	UCSC
CAGEd-oPOSSUM:	link
ZENBU report :	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  SAMD00021110 Library accession numbers Library id Method Exp. accession id Run accession id CNhs14096 CAGE DRX023727 DRR026126 CNhs14120 CAGE DRX023728 DRR026127 CNhs14048 CAGE DRX023731 DRR026130 CNhs14072 CAGE DRX023732 DRR026131 CNhs14145 CAGE DRX023733 DRR026132 CNhs14161 CAGE DRX023734 DRR026133 CNhs14185 CAGE DRX023735 DRR026134 CNhs14209 CAGE DRX023738 DRR026137 CNhs14409 CAGE DRX023740 DRR026139 CNhs14433 CAGE DRX023741 DRR026140 CNhs14521 CAGE DRX023742 DRR026141 CNhs14545 CAGE DRX023743 DRR026142 CNhs14569 CAGE DRX023744 DRR026143 CNhs14593 CAGE DRX023745 DRR026144 CNhs14457 CAGE DRX023748 DRR026147 CNhs14377 CAGE DRX023755 DRR026154 CNhs14401 CAGE DRX024299 DRR026704 Accession ID Mm9 Library id BAM CTSS CNhs14096 DRZ005378 DRZ006164 CNhs14120 DRZ005379 DRZ006165 CNhs14048 DRZ005382 DRZ006168 CNhs14072 DRZ005383 DRZ006169 CNhs14145 DRZ005384 DRZ006170 CNhs14161 DRZ005385 DRZ006171 CNhs14185 DRZ005386 DRZ006172 CNhs14209 DRZ005389 DRZ006175 CNhs14409 DRZ005391 DRZ006177 CNhs14433 DRZ005392 DRZ006178 CNhs14521 DRZ005393 DRZ006179 CNhs14545 DRZ005394 DRZ006180 CNhs14569 DRZ005395 DRZ006181 CNhs14593 DRZ005396 DRZ006182 CNhs14457 DRZ005399 DRZ006185 CNhs14377 DRZ005406 DRZ006192 CNhs14401 DRZ005956 DRZ006736 Accession ID Mm10 Library id BAM CTSS CNhs14096 CNhs14120 CNhs14048 CNhs14072 CNhs14145 CNhs14161 CNhs14185 CNhs14209 CNhs14409 CNhs14433 CNhs14521 CNhs14545 CNhs14569 CNhs14593 CNhs14457 CNhs14377 CNhs14401 DRZ010571 DRZ011229

Download raw sequence, BAM & CTSS
Mm9 Fasta BAM CTSS download download donwload Mm10 BAM CTSS download 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
FF:0000343 control treatment sample
FF:0011374 mouse whole body- embryo E17.5 sample

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

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)
0000343 (control treatment 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)