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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0001134,UBERON:0002100,UBERON:0000483,UBERON:0000926,UBERON:0000479,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0005423,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0000490,UBERON:0005291,UBERON:0002036,UBERON:0002385,UBERON:0000486,UBERON:0003104,UBERON:0000914,UBERON:0005256,UBERON:0006598,UBERON:0001015,UBERON:0002532,UBERON:0002329,UBERON:0002204,UBERON:0000383,UBERON:0003077,UBERON:0004290,UBERON:0009142,UBERON:0006603,UBERON:0003082,UBERON:0003059,UBERON:0007282,UBERON:0009618,UBERON:0007285
|DRA_sample_Accession=CAGE@SAMD00005073
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000055,CL:0000144,CL:0000723,CL:0000048,CL:0000548,CL:0000034,CL:0000012,CL:0000680,CL:0002321,CL:0002371,CL:0000393,CL:0000183,CL:0000187,CL:0000220,CL:0000004,CL:0000211,CL:0000056,CL:0000255,CL:0000188,CL:0000222,CL:0000355
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005073
|accession_numbers=CAGE;DRX008453;DRR009325;DRZ000750;DRZ002135;DRZ012100;DRZ013485
|accession_numbers_RNASeq=sRNA-Seq;DRX037053;DRR041419;DRZ007061
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001134,UBERON:0000479,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002036,UBERON:0002385,UBERON:0010317,UBERON:0001015,UBERON:0002204,UBERON:0000383
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000393,CL:0000183,CL:0000187,CL:0000211,CL:0000255,CL:0000188
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000002,FF:0000101,FF:0000001,FF:0000162
|comment=
|comment=
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000188
|ffid_belonging_in_development=CL:0000355,CL:0000222
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Skeletal%2520Muscle%2520Cells%252c%2520donor2.CNhs11983.11358-117H8.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Skeletal%2520Muscle%2520Cells%252c%2520donor2.CNhs11983.11358-117H8.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Skeletal%2520Muscle%2520Cells%252c%2520donor2.CNhs11983.11358-117H8.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Skeletal%2520Muscle%2520Cells%252c%2520donor2.CNhs11983.11358-117H8.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Skeletal%2520Muscle%2520Cells%252c%2520donor2.CNhs11983.11358-117H8.hg38.nobarcode.ctss.bed.gz
|id=FF:11358-117H8
|id=FF:11358-117H8
|is_a=EFO:0002091;;FF:0000162
|is_a=EFO:0002091;;FF:0000162
|is_obsolete=
|is_obsolete=
|library_id=CNhs11983
|library_id_phase_based=2:CNhs11983
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11358
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10004.GAGTGG.11358
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11358
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10004.GAGTGG.11358
|name=Skeletal Muscle Cells, donor2
|name=Skeletal Muscle Cells, donor2
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs11983,LSID836,release011,COMPLETED
|profile_hcage=CNhs11983,LSID836,release011,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=SRhi10004,,,
|profile_srnaseq=SRhi10004,,,
|rna_box=117
|rna_box=117
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|rna_tube_id=117H8
|rna_tube_id=117H8
|rna_weight_ug=10
|rna_weight_ug=10
|rnaseq_library_id=SRhi10004.GAGTGG
|sample_age=embryo 20week
|sample_age=embryo 20week
|sample_category=primary cells
|sample_cell_catalog=N/A
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_line=
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|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11358-117H8;search_select_hide=table117:FF:11358-117H8
}}
}}

Latest revision as of 17:55, 4 June 2020

Name:Skeletal Muscle Cells, donor2
Species:Human (Homo sapiens)
Library ID:CNhs11983
Sample type:primary cells
Genomic View: UCSC
FANTOM CAT:1
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueskeletal muscle
dev stage20 weeks old fetus
sexfemale
ageembryo 20week
cell typeskeletal muscle cell
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1432
catalog numberCA150-R10f
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005073
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11983 CAGE DRX008453 DRR009325
Accession ID Hg19

Library idBAMCTSS
CNhs11983 DRZ000750 DRZ002135
Accession ID Hg38

Library idBAMCTSS
CNhs11983 DRZ012100 DRZ013485
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005073
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10004.GAGTGG sRNA-Seq DRX037053 DRR041419
Accession ID Hg19

Library idBAMCTSS
SRhi10004.GAGTGG DRZ007061





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: CNhs11983This 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: CNhs11983This 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: CNhs11983


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)
0000211 (electrically active cell)
0000255 (eukaryotic cell)
0000188 (cell of skeletal muscle)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001134 (skeletal muscle tissue)
0000479 (tissue)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002036 (striated muscle tissue)
0002385 (muscle tissue)
0010317 (germ layer / neural crest derived structure)
0001015 (musculature)
0002204 (musculoskeletal system)
0000383 (musculature of body)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000162 (human skeletal 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)

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