FF:11291-117A4: Difference between revisions
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{{f5samples|DRA_sample_Accession=CAGE@ | {{f5samples | ||
|DRA_sample_Accession=CAGE@SAMD00006015 | |||
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00006015 | |||
|accession_numbers=CAGE;DRX008516;DRR009388;DRZ000813;DRZ002198;DRZ012163;DRZ013548 | |||
|accession_numbers_RNASeq=sRNA-Seq;DRX037103;DRR041469;DRZ007111 | |||
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000483,UBERON:0002384,UBERON:0000479,UBERON:0000064,UBERON:0000062,UBERON:0004120,UBERON:0004457,UBERON:0000061,UBERON:0000465,UBERON:0004923,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0006914,UBERON:0004905,UBERON:0000486,UBERON:0006915,UBERON:0007616,UBERON:0000042,UBERON:0000982,UBERON:0004458,UBERON:0010317,UBERON:0002217,UBERON:0002018,UBERON:0002204,UBERON:0001434,UBERON:0004770 | |||
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000151,CL:0002320,CL:0000066,CL:0002371,CL:0000213,CL:0002078,CL:0000499,CL:0000153,CL:0000327,CL:0000447,CL:0000215,CL:0000255,CL:0000214 | |||
|ancestors_in_disease_facet= | |||
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000002,FF:0000101,FF:0000001,FF:0000187 | |||
|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/CL:0000151;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000153;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000213;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000214;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000222;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000327;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000499;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0002078;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0000982;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0006914 | |||
|ffid_belonging_in_development=CL:0000134,CL:0000222 | |||
|fonse_cell_line= | |||
|fonse_cell_line_closure= | |||
|fonse_cellprecursor=CL:0000134,CL:0000222 | |||
|fonse_cellprecursor_closure=CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000220,CL:0000222,CL:0000255,CL:0000548,CL:0000723,CL:0002320,CL:0002321,CL:0002371 | |||
|fonse_developsfrom= | |||
|fonse_developsfrom_closure= | |||
|fonse_disease= | |||
|fonse_disease_closure= | |||
|fonse_isa=EFO:0002091,FF:0000187 | |||
|fonse_isa_closure=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000151,CL:0000153,CL:0000213,CL:0000214,CL:0000215,CL:0000255,CL:0000327,CL:0000447,CL:0000499,CL:0000548,CL:0002078,CL:0002320,CL:0002371,EFO:0000001,EFO:0000683,EFO:0002091,FF:0000001,FF:0000002,FF:0000101,FF:0000102,FF:0000187,FF:0000210,FF:11291-117A4,snap:Role,snap:SpecificallyDependentContinuant | |||
|fonse_location=UBERON:0002018 | |||
|fonse_location_closure=UBERON:0000042,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000119,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000486,UBERON:0000982,UBERON:0001062,UBERON:0001434,UBERON:0002018,UBERON:0002204,UBERON:0002217,UBERON:0002384,UBERON:0004120,UBERON:0004457,UBERON:0004458,UBERON:0004765,UBERON:0004770,UBERON:0004905,UBERON:0004923,UBERON:0006914,UBERON:0006915,UBERON:0007616 | |||
|fonse_organ= | |||
|fonse_organ_closure=UBERON:0000982,UBERON:0002217,UBERON:0004765 | |||
|fonse_organismsubdivision= | |||
|fonse_organismsubdivision_closure= | |||
|fonse_sampletype=FF:0000002 | |||
|fonse_sampletype_closure=FF:0000002 | |||
|fonse_stage= | |||
|fonse_stage_closure= | |||
|fonse_system= | |||
|fonse_system_closure=UBERON:0001434,UBERON:0002204 | |||
|fonse_taxon=FF:0000210 | |||
|fonse_taxon_closure=FF:0000210 | |||
|fonse_treatment= | |||
|fonse_treatment_closure= | |||
|has_quality= | |||
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Synoviocyte%252c%2520donor1.CNhs11068.11291-117A4.hg19.nobarcode.bam | |||
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Synoviocyte%252c%2520donor1.CNhs11068.11291-117A4.hg19.ctss.bed.gz | |||
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Synoviocyte%252c%2520donor1.CNhs11068.11291-117A4.hg19.nobarcode.rdna.fa.gz | |||
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Synoviocyte%252c%2520donor1.CNhs11068.11291-117A4.hg38.nobarcode.bam | |||
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Synoviocyte%252c%2520donor1.CNhs11068.11291-117A4.hg38.nobarcode.ctss.bed.gz | |||
|id=FF:11291-117A4 | |||
|is_a=EFO:0002091;;FF:0000187 | |||
|is_obsolete= | |||
|library_id=CNhs11068 | |||
|library_id_phase_based=2:CNhs11068 | |||
|microRNAs= | |||
|microRNAs_nn= | |||
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11291 | |||
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10007.GTCCGC.11291 | |||
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11291 | |||
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10007.GTCCGC.11291 | |||
|name=Synoviocyte, donor1 | |||
|namespace=FANTOM5 | |||
|part_of= | |||
|profile_cagescan=,,, | |||
|profile_hcage=CNhs11068,LSID723,release008,COMPLETED | |||
|profile_rnaseq= | |||
|profile_srnaseq=SRhi10007,,, | |||
|rna_box=117 | |||
|rna_catalog_number=CA408-R10a | |||
|rna_concentration=0.91 | |||
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0 | |||
|rna_lot_number=2506 | |||
|rna_od260/230= | |||
|rna_od260/280= | |||
|rna_position=A4 | |||
|rna_rin= | |||
|rna_sample_type=total RNA | |||
|rna_tube_id=117A4 | |||
|rna_weight_ug=10 | |||
|rnaseq_library_id=SRhi10007.GTCCGC | |||
|sample_age=57 | |||
|sample_category=primary cells | |||
|sample_cell_catalog=N/A | |||
|sample_cell_line= | |||
|sample_cell_lot=N/A | |||
|sample_cell_type=synovial cell | |||
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest) | |||
|sample_company=Cell Applications | |||
|sample_description= | |||
|sample_dev_stage=57 years old adult | |||
|sample_disease= | |||
|sample_donor(cell lot)= | |||
|sample_ethnicity=C | |||
|sample_experimental_condition= | |||
|sample_id=11291 | |||
|sample_note= | |||
|sample_sex=female | |||
|sample_species=Human (Homo sapiens) | |||
|sample_strain= | |||
|sample_tissue=synovium | |||
|top_motifs= | |||
|xref= | |||
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11291-117A4;search_select_hide=table117:FF:11291-117A4 | |||
}} | |||
Latest revision as of 16:31, 3 June 2020
| Name: | Synoviocyte, donor1 |
|---|---|
| Species: | Human (Homo sapiens) |
| Library ID: | CNhs11068 |
| Sample type: | primary cells |
| Genomic View: | UCSC |
| FANTOM CAT: | 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 |
| CAGEd-oPOSSUM: | link |
| ZENBU report : | link |
| Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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| Download raw sequence, BAM & CTSS | ||||||||||||||
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| RNA-Seq Accession numbers | ||||||||||||||||||||||||||||||||
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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
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: CNhs11068This 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: CNhs11068This 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: CNhs11068
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
EFO:0002091 biological replicate
FF:0000187 human synovial cell 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
CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000151 (secretory cell)
0002320 (connective tissue cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000213 (lining cell)
0002078 (meso-epithelial cell)
0000499 (stromal cell)
0000153 (GAG secreting cell)
0000327 (extracellular matrix secreting cell)
0000447 (carbohydrate secreting cell)
0000215 (barrier cell)
0000255 (eukaryotic cell)
0000214 (synovial cell)
UBERON: Anatomy
0000468 (multi-cellular organism)
0000483 (epithelium)
0002384 (connective tissue)
0000479 (tissue)
0000064 (organ part)
0000062 (organ)
0004120 (mesoderm-derived structure)
0004457 (cavity lining)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0004923 (organ component layer)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0006914 (squamous epithelium)
0004905 (articulation)
0000486 (multilaminar epithelium)
0006915 (stratified squamous epithelium)
0007616 (layer of synovial tissue)
0000042 (serous membrane)
0000982 (skeletal joint)
0004458 (body cavity or lining)
0010317 (germ layer / neural crest derived structure)
0002217 (synovial joint)
0002018 (synovial membrane of synovial joint)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0004770 (articular system)
FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000187 (human synovial cell 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
CL:0000134 (mesenchymal cell)
CL:0000222 (mesodermal cell)
