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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021190
|accession_numbers=CAGE;DRX022766;DRR025105;DRZ003530;DRZ004413;DRZ008271;DRZ009154
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_disease_facet=DOID:4,DOID:162,DOID:14566,DOID:0050687,DOID:3350,DOID:6193
|ancestors_in_disease_facet=DOID:4,DOID:162,DOID:14566,DOID:0050687,DOID:3350,DOID:6193
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001
|comment=
|comment=
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|expression_enrichment_score=
|expression_enrichment_score=
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|id=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/epithelioid%2520sarcoma%2520cell%2520line%253aHS-ES-2R.CNhs14239.10495-107B9.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/epithelioid%2520sarcoma%2520cell%2520line%253aHS-ES-2R.CNhs14239.10495-107B9.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.cell_line.hCAGE/epithelioid%2520sarcoma%2520cell%2520line%253aHS-ES-2R.CNhs14239.10495-107B9.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/epithelioid%2520sarcoma%2520cell%2520line%253aHS-ES-2R.CNhs14239.10495-107B9.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.cell_line.hCAGE/epithelioid%2520sarcoma%2520cell%2520line%253aHS-ES-2R.CNhs14239.10495-107B9.hg38.nobarcode.ctss.bed.gz
|id=FF:10495-107B9
|is_a=DOID:6193;;EFO:0002091;;FF:0000003;;FF:0000210
|is_a=DOID:6193;;EFO:0002091;;FF:0000003;;FF:0000210
|is_obsolete=
|is_obsolete=
|name=
|library_id=CNhs14239
|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;10495
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;10495
|name=epithelioid sarcoma cell line:HS-ES-2R
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=
|profile_cagescan=
|profile_hcage=
|profile_hcage=CNhs14239,LSID1178,release016,COMPLETED
|profile_rnaseq=
|profile_rnaseq=
|profile_srnaseq=
|profile_srnaseq=
|rna_box=
|rna_box=107
|rna_catalog_number=
|rna_catalog_number=
|rna_concentration=
|rna_concentration=1.04617
|rna_extraction_protocol=
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_lot_number=
|rna_od260/230=
|rna_od260/230=2.05
|rna_od260/280=
|rna_od260/280=2.11
|rna_position=
|rna_position=B9
|rna_rin=
|rna_rin=
|rna_sample_type=
|rna_sample_type=total RNA
|rna_tube_id=
|rna_tube_id=107B9
|rna_weight_ug=
|rna_weight_ug=26.15425
|sample_age=
|sample_age=
|sample_cell_catalog=
|sample_category=cell lines
|sample_cell_line=
|sample_cell_catalog=RCB2361
|sample_cell_line=HS-ES-2R
|sample_cell_lot=
|sample_cell_lot=
|sample_cell_type=
|sample_cell_type=unclassifiable
|sample_collaboration=
|sample_collaboration=Yukio Nakamura (RIKEN BRC)
|sample_company=
|sample_company=RIKEN Bioresource centre
|sample_description=
|sample_description=
|sample_dev_stage=
|sample_dev_stage=
|sample_disease=
|sample_disease=epithelioid sarcoma
|sample_donor(cell lot)=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_ethnicity=
|sample_experimental_condition=
|sample_experimental_condition=
|sample_id=
|sample_id=10495
|sample_note=
|sample_note=
|sample_sex=
|sample_sex=unknown
|sample_species=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_strain=
|sample_tissue=
|sample_tissue=ANATOMICAL SYSTEM
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:10495-107B9;search_select_hide=table117:FF:10495-107B9
}}
}}

Latest revision as of 14:27, 3 June 2020


Name:epithelioid sarcoma cell line:HS-ES-2R
Species:Human (Homo sapiens)
Library ID:CNhs14239
Sample type:cell lines
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexunknown
ageNA
cell typeunclassifiable
cell lineHS-ES-2R
companyRIKEN Bioresource centre
collaborationYukio Nakamura (RIKEN BRC)
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  SAMD00021190
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14239 CAGE DRX022766 DRR025105
Accession ID Hg19

Library idBAMCTSS
CNhs14239 DRZ003530 DRZ004413
Accession ID Hg38

Library idBAMCTSS
CNhs14239 DRZ008271 DRZ009154
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: CNhs14239This 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: CNhs14239This 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: CNhs14239


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)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
3350 (mesenchymal cell neoplasm)
6193 (epithelioid sarcoma)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (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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