Personal tools

FF:12871-137E9: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00021587
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00021587
|accession_numbers=CAGE;DRX023012;DRR025351;DRZ003776;DRZ004659;DRZ008517;DRZ009400
|accession_numbers_RNASeq=sRNA-Seq;DRX037323;DRR041689;DRZ007331
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001474,UBERON:0002384,UBERON:0000479,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0002204,UBERON:0001434
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001474,UBERON:0002384,UBERON:0000479,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0004765,UBERON:0002204,UBERON:0001434
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000055,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000062
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000055,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000062
Line 7: Line 11:
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|donor= biol_rep3 (A3 T13)
|ffid_belonging_in_development=CL:0000134,CL:0000335
|ffid_belonging_in_development=CL:0000134,CL:0000335
|fonse_cell_line=FF:0100385
|fonse_cell_line=FF:0100385
Line 36: Line 43:
|fonse_treatment_closure=EFO:0000369,FF:0000332,FF:0000606,FF:12871-137E9
|fonse_treatment_closure=EFO:0000369,FF:0000332,FF:0000606,FF:12871-137E9
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Saos-2%2520osteosarcoma%2520treated%2520with%2520ascorbic%2520acid%2520and%2520BGP%2520to%2520induce%2520calcification%252c%2520day04%252c%2520biol_rep3%2520%2528A3%2520T13%2529.CNhs12887.12871-137E9.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Saos-2%2520osteosarcoma%2520treated%2520with%2520ascorbic%2520acid%2520and%2520BGP%2520to%2520induce%2520calcification%252c%2520day04%252c%2520biol_rep3%2520%2528A3%2520T13%2529.CNhs12887.12871-137E9.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Saos-2%2520osteosarcoma%2520treated%2520with%2520ascorbic%2520acid%2520and%2520BGP%2520to%2520induce%2520calcification%252c%2520day04%252c%2520biol_rep3%2520%2528A3%2520T13%2529.CNhs12887.12871-137E9.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Saos-2%2520osteosarcoma%2520treated%2520with%2520ascorbic%2520acid%2520and%2520BGP%2520to%2520induce%2520calcification%252c%2520day04%252c%2520biol_rep3%2520%2528A3%2520T13%2529.CNhs12887.12871-137E9.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Saos-2%2520osteosarcoma%2520treated%2520with%2520ascorbic%2520acid%2520and%2520BGP%2520to%2520induce%2520calcification%252c%2520day04%252c%2520biol_rep3%2520%2528A3%2520T13%2529.CNhs12887.12871-137E9.hg38.nobarcode.ctss.bed.gz
|id=FF:12871-137E9
|id=FF:12871-137E9
|is_a=EFO:0002091;;FF:0000606
|is_a=EFO:0002091;;FF:0000606
|is_obsolete=
|is_obsolete=
|name=Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification, day04, biol_rep3 (A3 T13)
|library_id=CNhs12887
|library_id_phase_based=2:CNhs12887
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;12871
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10066.GCCAAT.12871
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;12871
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10066.GCCAAT.12871
|name=Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs12887,LSID974,release012,COMPLETED
|profile_hcage=CNhs12887,LSID974,release012,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=,,,
|profile_srnaseq=,,,
|rna_box=137
|rna_box=137
|rna_catalog_number=
|rna_catalog_number=
|rna_concentration=1.00
|rna_concentration=1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_lot_number=
Line 56: Line 76:
|rna_rin=
|rna_rin=
|rna_sample_type=
|rna_sample_type=
|rna_tube_id=137E9
|rna_tube_id=1.37E+11
|rna_weight_ug=10.00
|rna_weight_ug=10
|rnaseq_library_id=SRhi10066.GCCAAT
|sample_age=
|sample_age=
|sample_category=time courses
|sample_category=time courses
Line 78: Line 99:
|sample_strain=
|sample_strain=
|sample_tissue=
|sample_tissue=
|time= day04
|timecourse=Saos_calcification
|top_motifs=
|top_motifs=
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:12871-137E9;search_select_hide=table117:FF:12871-137E9
}}
}}

Latest revision as of 18:47, 4 June 2020


Name:Saos-2 osteosarcoma treated with ascorbic acid and BGP to induce calcification
Species:Human (Homo sapiens)
Library ID:CNhs12887
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexfemale
ageNA
cell typeosteoblast
cell lineSaos-2
companyNA
collaborationKim Summers (Roslin Institute)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021587
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12887 CAGE DRX023012 DRR025351
Accession ID Hg19

Library idBAMCTSS
CNhs12887 DRZ003776 DRZ004659
Accession ID Hg38

Library idBAMCTSS
CNhs12887 DRZ008517 DRZ009400
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00021587
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10066.GCCAAT sRNA-Seq DRX037323 DRR041689
Accession ID Hg19

Library idBAMCTSS
SRhi10066.GCCAAT DRZ007331





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: CNhs12887This 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: CNhs12887This 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: CNhs12887


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)
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)
0000384 (4 days sample)
0100385 (bone cancer cell line sample)
0100407 (osteosarcoma cell line sample)
0000606 (human Saos2 osteosarcoma cell line 4d 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)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:12871-137E9&oldid=4577358"