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{{f5samples
{{f5samples
|id=FF:10295-104G7
|DRA_sample_Accession=CAGE@SAMD00004699
|name=cruciate ligament, donor2
|accession_numbers=CAGE;DRX008641;DRR009513;DRZ000938;DRZ002323;DRZ012288;DRZ013673
|sample_id=10295
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0007023,UBERON:0006659,UBERON:0002384,UBERON:0000479,UBERON:0000026,UBERON:0000475,UBERON:0004120,UBERON:0007846,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0008784,UBERON:0001062,UBERON:0000480,UBERON:0006058,UBERON:0004905,UBERON:0004174,UBERON:0011139,UBERON:0004708,UBERON:0002101,UBERON:0004709,UBERON:0000982,UBERON:0002529,UBERON:0010538,UBERON:0003589,UBERON:0003569,UBERON:0003587,UBERON:0008846,UBERON:0003657,UBERON:0010317,UBERON:0003840,UBERON:0011088,UBERON:0007845,UBERON:0000211,UBERON:0010758,UBERON:0010707,UBERON:0003577,UBERON:0002217,UBERON:0002204,UBERON:0001434,UBERON:0000978,UBERON:0002103,UBERON:0004770,UBERON:0001465,UBERON:0000154,UBERON:0010709,UBERON:0001485
|rna_tube_id=
|rna_box=104
|rna_position=G7
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=2-Cl
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=cruciate ligament
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=
|sample_ethnicity=
|rna_rin=2.70000
|rna_od260/230=1.35000
|rna_od260/280=2.06000
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=Alessandro Bonetti
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=4.23640
|rna_concentration=
|sample_note=
|profile_hcage=CNhs13439,LSID1024,,SEQUENCING QUEUE
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000211,UBERON:0000465,UBERON:0000468,UBERON:0000479,UBERON:0001062,UBERON:0002384,UBERON:0006659,UBERON:0007023
|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,FF:0011152
 
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|f5samples=
|ffid_belonging_in_development=UBERON:0002532,UBERON:0006603,UBERON:0010316
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 40:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/cruciate%2520ligament%252c%2520donor2.CNhs13439.10295-104G7.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/cruciate%2520ligament%252c%2520donor2.CNhs13439.10295-104G7.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.tissue.hCAGE/cruciate%2520ligament%252c%2520donor2.CNhs13439.10295-104G7.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/cruciate%2520ligament%252c%2520donor2.CNhs13439.10295-104G7.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.tissue.hCAGE/cruciate%2520ligament%252c%2520donor2.CNhs13439.10295-104G7.hg38.nobarcode.ctss.bed.gz
|id=FF:10295-104G7
|is_a=EFO:0002091;;FF:0011152
|is_obsolete=
|library_id=CNhs13439
|library_id_phase_based=2:CNhs13439
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10295
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10295
|name=cruciate ligament, donor2
|namespace=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs13439,LSID1024,release012,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=104
|rna_catalog_number=
|rna_concentration=0.42364
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=2-Cl
|rna_od260/230=1.35
|rna_od260/280=2.06
|rna_position=G7
|rna_rin=2.7
|rna_sample_type=total RNA
|rna_tube_id=104G7
|rna_weight_ug=4.2364
|sample_age=
|sample_category=tissues
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=Alessandro Bonetti
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10295
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=cruciate ligament
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10295-104G7;search_select_hide=table117:FF:10295-104G7
}}
}}

Latest revision as of 13:58, 3 June 2020


Name:cruciate ligament, donor2
Species:Human (Homo sapiens)
Library ID:CNhs13439
Sample type:tissues
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuecruciate ligament
dev stageNA
sexmale
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationAlessandro Bonetti
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number2-Cl
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00004699
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13439 CAGE DRX008641 DRR009513
Accession ID Hg19

Library idBAMCTSS
CNhs13439 DRZ000938 DRZ002323
Accession ID Hg38

Library idBAMCTSS
CNhs13439 DRZ012288 DRZ013673
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

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: CNhs13439This 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: CNhs13439This 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: CNhs13439


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)
0006659 (cruciate ligament of knee)
0002384 (connective tissue)
0000479 (tissue)
0000026 (appendage)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0007846 (dense regular connective tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0008784 (lower limb segment)
0001062 (anatomical entity)
0000480 (anatomical group)
0006058 (multi-limb segment region)
0004905 (articulation)
0004174 (leg joint)
0011139 (synovial limb joint)
0004708 (paired limb/fin)
0002101 (limb)
0004709 (pelvic appendage)
0000982 (skeletal joint)
0002529 (limb segment)
0010538 (paired limb/fin segment)
0003589 (hindlimb connective tissue)
0003569 (leg connective tissue)
0003587 (limb connective tissue)
0008846 (skeletal ligament)
0003657 (limb joint)
0010317 (germ layer / neural crest derived structure)
0003840 (hindlimb joint)
0011088 (ligament of knee joint)
0007845 (regular connective tissue)
0000211 (ligament)
0010758 (subdivision of organism along appendicular axis)
0010707 (appendage girdle complex)
0003577 (knee connective tissue)
0002217 (synovial joint)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0000978 (leg)
0002103 (hindlimb)
0004770 (articular system)
0001465 (knee)
0000154 (posterior region of body)
0010709 (pelvic complex)
0001485 (knee joint)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000998 (adult tissue sample)
0000004 (tissue sample)
0011152 (human cruciate ligament 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:0006603 (presumptive mesoderm)
UBERON:0010316 (germ layer / neural crest)

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