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{{f5samples
{{f5samples
|id=FF:11258-116F7
|DRA_sample_Accession=CAGE@SAMD00005085
|name=Smooth Muscle Cells - Uterine, donor1
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005085
|sample_id=11258
|accession_numbers=CAGE;DRX008514;DRR009386;DRZ000811;DRZ002196;DRZ012161;DRZ013546
|rna_tube_id=116F7
|accession_numbers_RNASeq=sRNA-Seq;DRX037083;DRR041449;DRZ007091
|rna_box=116
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000995,UBERON:0003134,UBERON:0005156,UBERON:0000062,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000990,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003133,UBERON:0003975,UBERON:0004175,UBERON:0010317,UBERON:0003100,UBERON:0000474
|rna_position=F7
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000393,CL:0000183,CL:0000187,CL:0000192,CL:0000211,CL:0000255,CL:0002601
|sample_cell_lot=lot:6F0020
|sample_cell_catalog=CC-2562
|sample_company=Lonza
|rna_lot_number=
|rna_catalog_number=N/A
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=56 years old adult
|sample_tissue=uterus
|sample_donor(cell lot)=
|sample_sex=female
|sample_age=56
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=1.30000
|rna_od260/280=2.05000
|sample_cell_type=smooth muscle cell
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=58.00000
|rna_concentration=2.30000
|sample_note=Originally library704 tailing failed, the remaining sample is being rerun
|profile_hcage=CNhs11921,LSID842,release011,MAPPING_mixup?
|profile_cagescan=,,,
|profile_srnaseq=SRhi10006,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000056,CL:0000144,CL:0000183,CL:0000187,CL:0000192,CL:0000211,CL:0000220,CL:0000222,CL:0000255,CL:0000355,CL:0000393,CL:0000514,CL:0000548,CL:0000680,CL:0000723,CL:0002321,CL:0002371,CL:0002601
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000119,UBERON:0000383,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000474,UBERON:0000475,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000486,UBERON:0000490,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0000990,UBERON:0000995,UBERON:0001015,UBERON:0001062,UBERON:0001134,UBERON:0002036,UBERON:0002050,UBERON:0002204,UBERON:0002329,UBERON:0002385,UBERON:0002532,UBERON:0003059,UBERON:0003077,UBERON:0003082,UBERON:0003100,UBERON:0003104,UBERON:0003133,UBERON:0003134,UBERON:0003975,UBERON:0004120,UBERON:0004175,UBERON:0004290,UBERON:0005156,UBERON:0005291,UBERON:0005423,UBERON:0005795,UBERON:0009142
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000002,FF:0000101,FF:0000001,FF:0000167,FF:0000185
 
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|ffid_belonging_in_development=CL:0000355,CL:0000222,CL:0000514
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 41:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Uterine%252c%2520donor1.CNhs11921.11258-116F7.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Uterine%252c%2520donor1.CNhs11921.11258-116F7.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Uterine%252c%2520donor1.CNhs11921.11258-116F7.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Uterine%252c%2520donor1.CNhs11921.11258-116F7.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Smooth%2520Muscle%2520Cells%2520-%2520Uterine%252c%2520donor1.CNhs11921.11258-116F7.hg38.nobarcode.ctss.bed.gz
|id=FF:11258-116F7
|is_a=EFO:0002091;;FF:0000185
|is_obsolete=
|library_id=CNhs11921
|library_id_phase_based=2:CNhs11921
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11258
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10006.GTCCGC.11258
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11258
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10006.GTCCGC.11258
|name=Smooth Muscle Cells - Uterine, donor1
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11921,LSID842,release011,COMPLETED
|profile_rnaseq=
|profile_srnaseq=SRhi10006,,,
|rna_box=116
|rna_catalog_number=N/A
|rna_concentration=2.3
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=1.3
|rna_od260/280=2.05
|rna_position=F7
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=116F7
|rna_weight_ug=58
|rnaseq_library_id=SRhi10006.GTCCGC
|sample_age=56
|sample_category=primary cells
|sample_cell_catalog=CC-2562
|sample_cell_line=
|sample_cell_lot=lot:6F0020
|sample_cell_type=smooth muscle cell
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Lonza
|sample_description=
|sample_dev_stage=56 years old adult
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=11258
|sample_note=Originally library704 tailing failed, the remaining sample is being rerun
|sample_sex=female
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=uterus
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11258-116F7;search_select_hide=table117:FF:11258-116F7
}}
}}

Latest revision as of 16:28, 3 June 2020


Name:Smooth Muscle Cells - Uterine, donor1
Species:Human (Homo sapiens)
Library ID:CNhs11921
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueuterus
dev stage56 years old adult
sexfemale
age56
cell typesmooth muscle cell
cell lineNA
companyLonza
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberN/A
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005085
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11921 CAGE DRX008514 DRR009386
Accession ID Hg19

Library idBAMCTSS
CNhs11921 DRZ000811 DRZ002196
Accession ID Hg38

Library idBAMCTSS
CNhs11921 DRZ012161 DRZ013546
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005085
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10006.GTCCGC sRNA-Seq DRX037083 DRR041449
Accession ID Hg19

Library idBAMCTSS
SRhi10006.GTCCGC DRZ007091





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: CNhs11921This 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: CNhs11921This 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: CNhs11921


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)
0002371 (somatic cell)
0000393 (electrically responsive cell)
0000183 (contractile cell)
0000187 (muscle cell)
0000192 (smooth muscle cell)
0000211 (electrically active cell)
0000255 (eukaryotic cell)
0002601 (uterine smooth muscle cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000995 (uterus)
0003134 (female reproductive organ)
0005156 (reproductive structure)
0000062 (organ)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000990 (reproductive system)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003133 (reproductive organ)
0003975 (internal female genitalia)
0004175 (internal genitalia)
0010317 (germ layer / neural crest derived structure)
0003100 (female organism)
0000474 (female reproductive system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000167 (smooth muscle cell sample)
0000185 (human uterine smooth muscle 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:0000355 (multi-potent skeletal muscle stem cell)
CL:0000222 (mesodermal cell)
CL:0000514 (smooth muscle myoblast)

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