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{{f5samples
{{f5samples
|id=FF:10722-110A2
|DRA_sample_Accession=CAGE@SAMD00005151
|name=leiomyosarcoma  cell line:Hs 5.T
|accession_numbers=CAGE;DRX007773;DRR008645;DRZ000070;DRZ001455;DRZ011420;DRZ012805
|sample_id=10722
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|rna_tube_id=110A2
|rna_box=110
|rna_position=A2
|sample_cell_lot=
|sample_cell_catalog=CRL-7822
|sample_company=ATCC
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=soft tissue
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=81
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=1.39
|rna_od260/280=1.95
|sample_cell_type=unclassifiable
|sample_cell_line=Hs 5.T
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=leiomyosarcoma
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=2.39382
|rna_concentration=0.08866
|sample_note=
|profile_hcage=CNhs12192,LSID845,release010,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|ancestors_in_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:14566,DOID:0050687,DOID:4230,DOID:0060100,DOID:4045,DOID:1115,DOID:1967
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:0060100,DOID:1115,DOID:14566,DOID:162,DOID:1967,DOID:4,DOID:4045,DOID:4230
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001,FF:0100400,FF:0102595
|sample_description=
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|f5samples=
|fonse_cell_line=FF:0100400
|fonse_cell_line=FF:0100400
|fonse_cell_line_closure=FF:0100400
|fonse_cell_line_closure=FF:0100400
Line 66: Line 39:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|is_a=DOID:1967;;EFO:0002091;;FF:0000003;;FF:0000210;;FF:0102595
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.LQhCAGE/leiomyosarcoma%2520cell%2520line%253aHs%25205%252eT.CNhs12192.10722-110A2.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.LQhCAGE/leiomyosarcoma%2520cell%2520line%253aHs%25205%252eT.CNhs12192.10722-110A2.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.LQhCAGE/leiomyosarcoma%2520cell%2520line%253aHs%25205%252eT.CNhs12192.10722-110A2.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.LQhCAGE/leiomyosarcoma%2520cell%2520line%253aHs%25205%252eT.CNhs12192.10722-110A2.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.LQhCAGE/leiomyosarcoma%2520cell%2520line%253aHs%25205%252eT.CNhs12192.10722-110A2.hg38.nobarcode.ctss.bed.gz
|id=FF:10722-110A2
|is_a=DOID:1967;;EFO:0002091;;FF:0000210;;FF:0102595
|is_obsolete=
|library_id=CNhs12192
|library_id_phase_based=2:CNhs12192
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;10722
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10722
|name=leiomyosarcoma cell line:Hs 5.T
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12192,LSID976,release010,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=110
|rna_catalog_number=
|rna_concentration=0.08866
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.39
|rna_od260/280=1.95
|rna_position=A2
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=110A2
|rna_weight_ug=2.39382
|sample_age=81
|sample_category=cell lines
|sample_cell_catalog=CRL-7822
|sample_cell_line=Hs 5.T
|sample_cell_lot=
|sample_cell_type=unclassifiable
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=ATCC
|sample_description=
|sample_dev_stage=
|sample_disease=leiomyosarcoma
|sample_donor(cell lot)=
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=10722
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=soft tissue
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10722-110A2;search_select_hide=table117:FF:10722-110A2
}}
}}

Latest revision as of 15:01, 3 June 2020


Name:leiomyosarcoma cell line:Hs 5.T
Species:Human (Homo sapiens)
Library ID:CNhs12192
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuesoft tissue
dev stageNA
sexfemale
age81
cell typeunclassifiable
cell lineHs 5.T
companyATCC
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
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  SAMD00005151
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12192 CAGE DRX007773 DRR008645
Accession ID Hg19

Library idBAMCTSS
CNhs12192 DRZ000070 DRZ001455
Accession ID Hg38

Library idBAMCTSS
CNhs12192 DRZ011420 DRZ012805
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: CNhs12192This 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: CNhs12192This 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: CNhs12192


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

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
4230 (smooth muscle cancer)
0060100 (musculoskeletal system cancer)
4045 (muscle cancer)
1115 (sarcoma)
1967 (leiomyosarcoma)

UBERON: Anatomy
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0100400 (sarcoma cell line sample)
0102595 (leiomyosarcoma cell line 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
NA

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