FF:10360-105E9

Name:	amygdala, newborn, donor10223
Species:	Human (Homo sapiens)
Library ID:
Sample type:	tissues
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information
Sample information strain NA tissue amygdala dev stage NA sex male age 0 cell type CELL MIXTURE - tissue sample cell line NA company NA collaboration Peter Heutink 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) OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
Method Sample accession id CAGE  SAMD00021169 Library accession numbers Library id Method Exp. accession id Run accession id CAGE DRX023561 DRR025956 Accession ID Hg19 Library id BAM CTSS DRZ004381 DRZ005208 Accession ID Hg38 Library id BAM CTSS

Download raw sequence, BAM & CTSS
Hg19 BAM CTSS [{{{hg19bam}}} download] [{{{hg19ctss}}} donwload] Hg38 BAM CTSS [{{{hg38bam}}} download] [{{{hg38ctss}}} 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>dataNo results for this sample

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
library id: CNhs14078This 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: CNhs14078This 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: CNhs14078

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0001372
FF:0000004 tissue sample
FF:0000210 human sample
UBERON:0001876 amygdala
UBERON:0007221 neonate stage

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)
0000955 (brain)
0001871 (temporal lobe)
0001876 (amygdala)
0000956 (cerebral cortex)
0000479 (tissue)
0007221 (neonate stage)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000092 (post-embryonic stage)
0000481 (multi-tissue structure)
0000105 (life cycle stage)
0000000 (processual entity)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0002619 (regional part of cerebral cortex)
0001062 (anatomical entity)
0000480 (anatomical group)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0000104 (life cycle)
0000066 (fully formed stage)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0000203 (pallium)
0001950 (neocortex)
0000349 (limbic system)
0010011 (collection of basal ganglia)
0000112 (juvenile stage)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000004 (tissue 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
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0010316 (germ layer / neural crest)