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{{f5samples
{{f5samples
|id=FF:13190-141E4
|DRA_sample_Accession=CAGE@SAMD00021824
|name=MCF7 breast cancer cell line response to HRG, 04hr, biol_rep3
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00021824
|sample_id=13190
|accession_numbers=CAGE;DRX022988;DRR025327;DRZ003752;DRZ004635;DRZ008493;DRZ009376
|rna_tube_id=141E4
|accession_numbers_RNASeq=sRNA-Seq;DRX037306;DRR041672;DRZ007314
|rna_box=141
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000310,UBERON:0002100,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0001062,UBERON:0009569,UBERON:0001443,UBERON:0000915
|rna_position=E4
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0000255
|sample_cell_lot=
|ancestors_in_disease_facet=DOID:4,DOID:0050686,DOID:162,DOID:14566,DOID:0050687,DOID:7,DOID:5093,DOID:305,DOID:299,DOID:1612
|sample_cell_catalog=
|ancestors_in_ff_facet=FF:0000102,FF:0000003,FF:0000210,FF:0000101,FF:0000001,FF:0000350,FF:0000361,FF:0100093,FF:0000331,FF:0100297,FF:0101912,FF:0101120,FF:0100816,FF:0100167,FF:0100356,FF:0000453
|sample_company=
|comment=
|rna_lot_number=
|created_by=
|rna_catalog_number=
|creation_date=
|sample_species=Human (Homo sapiens)
|data_phase=2
|sample_strain=
|datafreeze_phase=2
|sample_dev_stage=
|def=
|sample_tissue=breast
|donor= biol_rep3
|sample_donor(cell lot)=rep3
|sample_sex=female
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=1.49000
|rna_od260/280=2.04000
|sample_cell_type=mammary gland epithelial cell
|sample_cell_line=MCF7
|sample_collaboration=Mariko Okada Hatakeyama (RIKEN RCAI)
|sample_experimental_condition=MCF7 breast cancer cell line response to Heregulin
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=Repurified by minelute
|rna_weight_ug=7.10100
|rna_concentration=0.71010
|sample_note=
|profile_hcage=CNhs12764,LSID971,release012,MAPPING
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000255,CL:0000548
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000310,UBERON:0000465,UBERON:0000468,UBERON:0000475,UBERON:0000915,UBERON:0001062,UBERON:0001443,UBERON:0005482
|ancestors_in_disease_facet=DOID:0050686,DOID:0050687,DOID:14566,DOID:1612,DOID:162,DOID:299,DOID:305,DOID:4,DOID:5093,DOID:7
|sample_description=
 
|fonse_cell_line=FF:0100816,FF:0101120
|fonse_cell_line=FF:0100816,FF:0101120
|fonse_cell_line_closure=FF:0100816,FF:0101120
|fonse_cell_line_closure=FF:0100816,FF:0101120
Line 67: Line 41:
|fonse_treatment=EFO:0000369,FF:0000331,FF:0000453,FF:13190-141E4
|fonse_treatment=EFO:0000369,FF:0000331,FF:0000453,FF:13190-141E4
|fonse_treatment_closure=EFO:0000369,FF:0000331,FF:0000453,FF:13190-141E4
|fonse_treatment_closure=EFO:0000369,FF:0000331,FF:0000453,FF:13190-141E4
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520HRG%252c%252004hr%252c%2520biol_rep3.CNhs12764.13190-141E4.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520HRG%252c%252004hr%252c%2520biol_rep3.CNhs12764.13190-141E4.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520HRG%252c%252004hr%252c%2520biol_rep3.CNhs12764.13190-141E4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520HRG%252c%252004hr%252c%2520biol_rep3.CNhs12764.13190-141E4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/MCF7%2520breast%2520cancer%2520cell%2520line%2520response%2520to%2520HRG%252c%252004hr%252c%2520biol_rep3.CNhs12764.13190-141E4.hg38.nobarcode.ctss.bed.gz
|id=FF:13190-141E4
|is_a=EFO:0002091;;FF:0000453
|is_obsolete=
|library_id=CNhs12764
|library_id_phase_based=2:CNhs12764
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;13190
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10064.TTAGGC.13190
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;13190
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10064.TTAGGC.13190
|name=MCF7 breast cancer cell line response to HRG
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12764,LSID971,release012,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=141
|rna_catalog_number=
|rna_concentration=0.71
|rna_extraction_protocol=Repurified by minelute
|rna_lot_number=
|rna_od260/230=1.49
|rna_od260/280=2.04
|rna_position=E4
|rna_rin=
|rna_sample_type=
|rna_tube_id=1.41E+06
|rna_weight_ug=7.1
|rnaseq_library_id=SRhi10064.TTAGGC
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_line=MCF7
|sample_cell_lot=
|sample_cell_type=mammary gland epithelial cell
|sample_collaboration=Mariko Okada Hatakeyama (RIKEN RCAI)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=rep3
|sample_ethnicity=
|sample_experimental_condition=MCF7 breast cancer cell line response to Heregulin
|sample_id=13190
|sample_note=
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=breast
|time= 04hr
|timecourse=MCF7_response_to_HRG
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:13190-141E4;search_select_hide=table117:FF:13190-141E4
}}
}}

Latest revision as of 18:53, 4 June 2020


Name:MCF7 breast cancer cell line response to HRG
Species:Human (Homo sapiens)
Library ID:CNhs12764
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebreast
dev stageNA
sexfemale
ageNA
cell typemammary gland epithelial cell
cell lineMCF7
companyNA
collaborationMariko Okada Hatakeyama (RIKEN RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)Repurified by minelute

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021824
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12764 CAGE DRX022988 DRR025327
Accession ID Hg19

Library idBAMCTSS
CNhs12764 DRZ003752 DRZ004635
Accession ID Hg38

Library idBAMCTSS
CNhs12764 DRZ008493 DRZ009376
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00021824
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10064.TTAGGC sRNA-Seq DRX037306 DRR041672
Accession ID Hg19

Library idBAMCTSS
SRhi10064.TTAGGC DRZ007314





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: CNhs12764This 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: CNhs12764This 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: CNhs12764


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

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0000255 (eukaryotic cell)

DOID: Disease
4 (disease)
0050686 (organ system cancer)
162 (cancer)
14566 (disease of cellular proliferation)
0050687 (cell type cancer)
7 (disease of anatomical entity)
5093 (thoracic cancer)
305 (carcinoma)
299 (adenocarcinoma)
1612 (breast cancer)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000310 (breast)
0002100 (trunk)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)
0009569 (subdivision of trunk)
0001443 (chest)
0000915 (thoracic segment of trunk)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000350 (experimentally modified sample)
0000361 (4 hr sample)
0100093 (MCF-7 cell sample)
0000331 (HRG treatment sample)
0100297 (carcinoma cell line sample)
0101912 (breast adenocarcinoma cell line sample)
0101120 (epithelial cell line sample)
0100816 (breast cell line sample)
0100167 (adenocarcinoma cell line sample)
0100356 (breast cancer cell line sample)
0000453 (human MCF7 breast cancer cell line 4h after HRG treatment 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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