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{{f5samples
{{f5samples
|id=FF:10372-105G3
|DRA_sample_Accession=CAGE@SAMD00021181
|name=putamen, adult, donor10258
|accession_numbers=CAGE;DRX023572;DRR025967;DRZ004392;DRZ005219;DRZ009133;DRZ009960!CAGE;DRX023587;DRR025982;DRZ004407;DRZ005234;DRZ009148;DRZ009975
|sample_id=10372
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0000955,UBERON:0001874,UBERON:0000369,UBERON:0002435,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0003528,UBERON:0002791,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0009663,UBERON:0002420,UBERON:0002616,UBERON:0002780,UBERON:0000125,UBERON:0002020,UBERON:0007245,UBERON:0010317,UBERON:0002308,UBERON:0010009,UBERON:0001017,UBERON:0001016,UBERON:0001869,UBERON:0001893,UBERON:0001890,UBERON:0005383,UBERON:0010011,UBERON:0000204,UBERON:0005382,UBERON:0000454
|rna_tube_id=105G3
|rna_box=105
|rna_position=G3
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=putamen
|sample_donor(cell lot)=donor: 10258
|sample_sex=female
|sample_age=89
|sample_ethnicity=
|rna_rin=8.2
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=Peter Heutink
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=
|rna_concentration=0.5
|sample_note=
|profile_hcage=CNhs14225,LSID1178,release016,COMPLETED
|profile_cagescan=
|profile_srnaseq=
|profile_rnaseq=
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000101,FF:0000001,FF:0000998,FF:0000004
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0000454;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0000955;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001016;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001874;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001890;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0001893;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0002308;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0002435;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0003528;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0005382;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0009663
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006601,UBERON:0010316
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 40:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|is_a=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/putamen%252c%2520adult%252c%2520donor10258%252c%2520tech_rep2.CNhs14618.10372-105G3.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/putamen%252c%2520adult%252c%2520donor10258%252c%2520tech_rep2.CNhs14618.10372-105G3.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/putamen%252c%2520adult%252c%2520donor10258%252c%2520tech_rep2.CNhs14618.10372-105G3.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/putamen%252c%2520adult%252c%2520donor10258%252c%2520tech_rep2.CNhs14618.10372-105G3.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/putamen%252c%2520adult%252c%2520donor10258%252c%2520tech_rep2.CNhs14618.10372-105G3.hg38.nobarcode.ctss.bed.gz
|id=FF:10372-105G3
|is_a=FF:0000210;;FF:0000998;;UBERON:0001874
|is_obsolete=
|library_id=CNhs14225!CNhs14618
|library_id_phase_based=2:
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10372
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10372
|name=putamen, adult, donor10258
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=
|profile_hcage=Cnhs14225&CNhs14618,LSID1178,release016,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=105
|rna_catalog_number=
|rna_concentration=0.5
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=G3
|rna_rin=8.2
|rna_sample_type=total RNA
|rna_tube_id=105G3
|rna_weight_ug=
|sample_age=89
|sample_category=tissues
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=Peter Heutink
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=donor: 10258
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10372
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=putamen
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10372-105G3;search_select_hide=table117:FF:10372-105G3
}}
}}

Latest revision as of 13:58, 3 June 2020

Name:putamen, adult, donor10258
Species:Human (Homo sapiens)
Library ID:CNhs14225,CNhs14618
Sample type:tissues
Genomic View: UCSC
FANTOM CAT:1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueputamen
dev stageNA
sexfemale
age89
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021181
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14225 CAGE DRX023572 DRR025967
CNhs14618 CAGE DRX023587 DRR025982
Accession ID Hg19

Library idBAMCTSS
CNhs14225 DRZ004392 DRZ005219
CNhs14618 DRZ004407 DRZ005234
Accession ID Hg38

Library idBAMCTSS
CNhs14225 DRZ009133 DRZ009960
CNhs14618 DRZ009148 DRZ009975
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload





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

No 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

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: Cnhs14225This sample isn't target for the analysis
library id: CNhs14618This 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: Cnhs14225This sample isn't target for the analysis
library id: CNhs14618This 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: Cnhs14225
library id: CNhs14618


FANTOM5 (FF) ontology

Direct parent terms


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)
0007023 (adult organism)
0000955 (brain)
0001874 (putamen)
0000369 (corpus striatum)
0002435 (striatum)
0000479 (tissue)
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)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0003528 (brain grey matter)
0002791 (regional part of telencephalon)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0009663 (telencephalic nucleus)
0002420 (basal ganglion)
0002616 (regional part of brain)
0002780 (regional part of forebrain)
0000125 (neural nucleus)
0002020 (gray matter)
0007245 (nuclear complex of neuraxis)
0010317 (germ layer / neural crest derived structure)
0002308 (nucleus of brain)
0010009 (aggregate regional part of brain)
0001017 (central nervous system)
0001016 (nervous system)
0001869 (cerebral hemisphere)
0001893 (telencephalon)
0001890 (forebrain)
0005383 (caudate-putamen)
0010011 (collection of basal ganglia)
0000204 (ventral part of telencephalon)
0005382 (dorsal striatum)
0000454 (cerebral subcortex)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue 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)

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