FF:11219-116B4

Name:	Mesenchymal Stem Cells - Vertebral, donor1
Species:	Human (Homo sapiens)
Library ID:	CNhs10846
Sample type:	primary cells
Genomic View:	UCSC
FANTOM CAT:	1, 2, 3, 4
CAGEd-oPOSSUM:	link

Additional information

Sample information strain NA tissue spinal cord dev stage NA sex NA age NA cell type mesenchymal stem cell cell line NA company Sciencell collaboration FANTOM5 OSC CORE (contact: Al Forrest) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number SC7555 sample type total RNA extraction protocol (Details) OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
Method Sample accession id CAGE  SAMD00004889 Library accession numbers Library id Method Exp. accession id Run accession id CNhs10846 CAGE DRX008344 DRR009216 Accession ID Hg19 Library id BAM CTSS CNhs10846 DRZ000641 DRZ002026 Accession ID Hg38 Library id BAM CTSS CNhs10846 DRZ011991 DRZ013376

Download raw sequence, BAM & CTSS
Hg19 Fasta BAM CTSS download download donwload Hg38 BAM CTSS download donwload

RNA-Seq Accession numbers
Method Sample accession id sRNA-Seq  SAMD00004889 Library accession numbers Library id Method Exp. accession id Run accession id SRhi10006.CAGATC sRNA-Seq DRX037074 DRR041440 Accession ID Hg19 Library id BAM CTSS SRhi10006.CAGATC DRZ007082 Accession ID Hg38 Library id BAM CTSS SRhi10006.CAGATC

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

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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: CNhs10846This 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: CNhs10846This 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: CNhs10846

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000093 human vertebral mesenchymal stem cell sample

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)
0000723 (somatic stem cell)
0000048 (multi fate stem cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000219 (motile cell)
0000134 (mesenchymal cell)
0000255 (eukaryotic cell)
0000034 (stem cell)
0002572 (vertebral mesenchymal stem cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001474 (bone element)
0002384 (connective tissue)
0000479 (tissue)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000075 (subdivision of skeletal system)
0004765 (skeletal element)
0002513 (endochondral bone)
0008001 (irregular bone)
0010913 (vertebral element)
0010363 (endochondral element)
0002412 (vertebra)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0011138 (post-cranial axial skeletal system)
0001130 (vertebral column)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000093 (human vertebral mesenchymal stem 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:0000134 (mesenchymal cell)