Personal tools

FF:11277-116H8: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:11277-116H8 |name=Osteoblast, donor1 |sample_id=11277 |rna_tube_id=116H8 |rna_box=116 |rna_position=H8 |sample_cell_lot=N/A |sample_cell_catalog=N/A...")
 
No edit summary
 
(22 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:11277-116H8
|DRA_sample_Accession=CAGE@SAMD00005515
|name=Osteoblast, donor1
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005515
|sample_id=11277
|accession_numbers=CAGE;DRX008392;DRR009264;DRZ000689;DRZ002074;DRZ012039;DRZ013424
|rna_tube_id=116H8
|accession_numbers_RNASeq=sRNA-Seq;DRX037258;DRR041624;DRZ007266
|rna_box=116
|ancestors_in_anatomy_facet=UBERON:0002384,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
|rna_position=H8
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000055,CL:0000003,CL:0000548,CL:0002320,CL:0002371,CL:0000255,CL:0000062
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=Cell Applications
|rna_lot_number=1266.00000
|rna_catalog_number=CA406-R10f
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=18 weeks old fetus
|sample_tissue=bone
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=18 week embryo
|sample_ethnicity=C
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=osteoblast
|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-TRIzol-isopropanol-v1.0
|rna_weight_ug=10.00000
|rna_concentration=1.00000
|sample_note=
|profile_hcage=CNhs11078,LSID724,release008,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=SRhi10015,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000035,CL:0000048,CL:0000055,CL:0000062,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000255,CL:0000335,CL:0000375,CL:0000548,CL:0000723,CL:0002320,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000465,UBERON:0000479,UBERON:0001062,UBERON:0002384
|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:0000127,FF:0000128
 
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|ffid_belonging_in_development=CL:0000134,CL:0000335
|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/Osteoblast%252c%2520donor1.CNhs11078.11277-116H8.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Osteoblast%252c%2520donor1.CNhs11078.11277-116H8.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Osteoblast%252c%2520donor1.CNhs11078.11277-116H8.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Osteoblast%252c%2520donor1.CNhs11078.11277-116H8.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Osteoblast%252c%2520donor1.CNhs11078.11277-116H8.hg38.nobarcode.ctss.bed.gz
|id=FF:11277-116H8
|is_a=EFO:0002091;;FF:0000127;;FF:0000128
|is_obsolete=
|library_id=CNhs11078
|library_id_phase_based=2:CNhs11078
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11277
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10015.ATGTCA.11277
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11277
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10015.ATGTCA.11277
|name=Osteoblast, donor1
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11078,LSID724,release008,COMPLETED
|profile_rnaseq=
|profile_srnaseq=SRhi10015,,,
|rna_box=116
|rna_catalog_number=CA406-R10f
|rna_concentration=1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
|rna_lot_number=1266
|rna_od260/230=
|rna_od260/280=
|rna_position=H8
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=116H8
|rna_weight_ug=10
|rnaseq_library_id=SRhi10015.ATGTCA
|sample_age=18 week embryo
|sample_category=primary cells
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=osteoblast
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Cell Applications
|sample_description=
|sample_dev_stage=18 weeks old fetus
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=C
|sample_experimental_condition=
|sample_id=11277
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=bone
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11277-116H8;search_select_hide=table117:FF:11277-116H8
}}
}}

Latest revision as of 16:30, 3 June 2020


Name:Osteoblast, donor1
Species:Human (Homo sapiens)
Library ID:CNhs11078
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuebone
dev stage18 weeks old fetus
sexmale
age18 week embryo
cell typeosteoblast
cell lineNA
companyCell Applications
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number1266
catalog numberCA406-R10f
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005515
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11078 CAGE DRX008392 DRR009264
Accession ID Hg19

Library idBAMCTSS
CNhs11078 DRZ000689 DRZ002074
Accession ID Hg38

Library idBAMCTSS
CNhs11078 DRZ012039 DRZ013424
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005515
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10015.ATGTCA sRNA-Seq DRX037258 DRR041624
Accession ID Hg19

Library idBAMCTSS
SRhi10015.ATGTCA DRZ007266





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: CNhs11078This 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: CNhs11078This 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: CNhs11078


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
0002384 (connective tissue)
0000479 (tissue)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0001062 (anatomical entity)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000127 (human osteoblast-Sciencell sample)
0000128 (human osteoblast-Cell applications 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:11277-116H8&oldid=4576331"