Personal tools

FF:13496-145C4: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:13496-145C4 |name= |sample_id=13496 |rna_tube_id=145C4 |rna_box=145 |rna_position=C4 |sample_cell_lot= |sample_cell_catalog= |sample_company= |rna_lot_numbe...")
 
No edit summary
 
(19 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:13496-145C4
|DRA_sample_Accession=CAGE@SAMD00022113
|name=
|accession_numbers=CAGE;DRX023487;DRR025882;DRZ004307;DRZ005134;DRZ009048;DRZ009875
|sample_id=13496
|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
|rna_tube_id=145C4
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000055,CL:0000003,CL:0000548,CL:0000680,CL:0002321,CL:0002371,CL:0000393,CL:0000183,CL:0000187,CL:0000211,CL:0000056,CL:0000255,CL:0000188,CL:0000737,CL:0000228,CL:0002372
|rna_box=145
|rna_position=C4
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=skeletal muscle
|sample_donor(cell lot)=DMD1_Mb
|sample_sex=male
|sample_age=3 years old
|sample_ethnicity=
|rna_rin=
|rna_od260/230=2.15
|rna_od260/280=2.08
|sample_cell_type=myoblast
|sample_cell_line=
|sample_collaboration=Beatrice Bodega/Valerio Orlando
|sample_experimental_condition=
|sample_disease=normal control
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=18.06
|rna_concentration=1.5
|sample_note=
|profile_hcage=CNhs13875,LSID1093,release015,SEQUENCING QUEUE
|profile_cagescan=
|profile_srnaseq=
|profile_rnaseq=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000210,FF:0000101,FF:0000001,FF:0200006
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|donor= Duchenne Muscular Dystrophy donor1
|fantom_cat=http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000056;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000187;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000515;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0000737;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/CL:0002372;;http://fantom.gsc.riken.jp/5/suppl/Hon_et_al_2016/vis/#/ontologies/UBERON:0002385
|ffid_belonging_in_development=CL:0000355,CL:0000222,CL:0000515
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: 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.timecourse.hCAGE/Myoblast%2520differentiation%2520to%2520myotubes%252c%2520day00%252c%2520Duchenne%2520Muscular%2520Dystrophy%2520donor1.CNhs14586.13496-145C4.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Myoblast%2520differentiation%2520to%2520myotubes%252c%2520day00%252c%2520Duchenne%2520Muscular%2520Dystrophy%2520donor1.CNhs14586.13496-145C4.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Myoblast%2520differentiation%2520to%2520myotubes%252c%2520day00%252c%2520Duchenne%2520Muscular%2520Dystrophy%2520donor1.CNhs14586.13496-145C4.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Myoblast%2520differentiation%2520to%2520myotubes%252c%2520day00%252c%2520Duchenne%2520Muscular%2520Dystrophy%2520donor1.CNhs14586.13496-145C4.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Myoblast%2520differentiation%2520to%2520myotubes%252c%2520day00%252c%2520Duchenne%2520Muscular%2520Dystrophy%2520donor1.CNhs14586.13496-145C4.hg38.nobarcode.ctss.bed.gz
|id=FF:13496-145C4
|is_a=FF:0000210;;FF:0200006
|is_obsolete=
|library_id=CNhs14586
|library_id_phase_based=2:CNhs14586
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;13496
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;13496
|name=Myoblast differentiation to myotubes
|namespace=
|part_of=
|profile_cagescan=
|profile_hcage=CNhs14586,LSID1335,release018,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=145
|rna_catalog_number=
|rna_concentration=1.50498
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=C4
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=145C4
|rna_weight_ug=18.0598
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_line=UNDEFINED_CELL_LINE
|sample_cell_lot=
|sample_cell_type=myoblast
|sample_collaboration=Beatrice Bodega, Valerio Orlando
|sample_company=
|sample_description=
|sample_dev_stage=UNDEFINED_DEV_STAGE
|sample_disease=normal control
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=UNDEFINED_CONDITION
|sample_id=13496
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=UNDEFINED_STRAIN
|sample_tissue=skeletal muscle
|time= day00
|timecourse=Myoblast_to_myotube_(wt_and_DMD)
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:13496-145C4;search_select_hide=table117:FF:13496-145C4
}}
}}

Latest revision as of 19:00, 4 June 2020

Name:Myoblast differentiation to myotubes
Species:Human (Homo sapiens)
Library ID:CNhs14586
Sample type:time courses
Genomic View: UCSC
FANTOM CAT:1, 2, 3, 4, 5, 6
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainUNDEFINED_STRAIN
tissueskeletal muscle
dev stageUNDEFINED_DEV_STAGE
sexmale
ageNA
cell typemyoblast
cell lineUNDEFINED_CELL_LINE
companyNA
collaborationBeatrice Bodega, Valerio Orlando
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00022113
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14586 CAGE DRX023487 DRR025882
Accession ID Hg19

Library idBAMCTSS
CNhs14586 DRZ004307 DRZ005134
Accession ID Hg38

Library idBAMCTSS
CNhs14586 DRZ009048 DRZ009875
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload





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: CNhs14586This 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: CNhs14586This 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: CNhs14586


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)
0000680 (muscle precursor cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0000393 (electrically responsive cell)
0000183 (contractile cell)
0000187 (muscle cell)
0000211 (electrically active cell)
0000056 (myoblast)
0000255 (eukaryotic cell)
0000188 (cell of skeletal muscle)
0000737 (striated muscle cell)
0000228 (multinucleate cell)
0002372 (myotube)

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
0000210 (human sample)
0000101 (sample by species)
0000001 (sample)
0200006 (myoblast differentiation to myotubes, control 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)
CL:0000515 (skeletal muscle myoblast)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=FF:13496-145C4&oldid=4577923"