FF:12764-136C1

Name:	Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification
Species:	Human (Homo sapiens)
Library ID:	CNhs12863
Sample type:	time courses
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information
Sample information strain NA tissue NA dev stage NA sex female age NA cell type osteoblast cell line Saos-2 company NA collaboration Kim Summers (Roslin Institute) External link for information [{{{sample_info_link}}} {{{sample_info_link}}}] RNA information lot number NA catalog number NA sample type NA extraction protocol (Details) OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
Method Sample accession id CAGE  SAMD00021501 Library accession numbers Library id Method Exp. accession id Run accession id CNhs12863 CAGE DRX022875 DRR025214 Accession ID Hg19 Library id BAM CTSS CNhs12863 DRZ003639 DRZ004522 Accession ID Hg38 Library id BAM CTSS CNhs12863 DRZ008380 DRZ009263

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  SAMD00021501 Library accession numbers Library id Method Exp. accession id Run accession id SRhi10066.ACTTGA sRNA-Seq DRX037325 DRR041691 Accession ID Hg19 Library id BAM CTSS SRhi10066.ACTTGA DRZ007333 Accession ID Hg38 Library id BAM CTSS SRhi10066.ACTTGA

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: CNhs12863This 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: CNhs12863This 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: CNhs12863

FANTOM5 (FF) ontology

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Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000597 human Saos2 osteosarcoma cell line 60min after induction of calcification with ascorbate and BPG 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)
0000055 (non-terminally differentiated cell)
0000003 (native cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0000255 (eukaryotic cell)
0000062 (osteoblast)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001474 (bone element)
0002384 (connective tissue)
0000479 (tissue)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0004765 (skeletal element)
0002204 (musculoskeletal system)
0001434 (skeletal system)

FF: FANTOM5
0000102 (sample by type)
0000003 (cell line sample)
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0000350 (experimentally modified sample)
0000332 (calcification induced with ascorbate and BPG sample)
0100971 (SAOS-2 cell sample)
0000349 (60 minutes sample)
0100385 (bone cancer cell line sample)
0100407 (osteosarcoma cell line sample)
0000597 (human Saos2 osteosarcoma cell line 60min after induction of calcification with ascorbate and BPG 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)
CL:0000335 (mesenchyme condensation cell)