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{{f5samples
{{f5samples
|id=FF:12514-133B3
|DRA_sample_Accession=CAGE@SAMD00021353
|name=Lymphatic Endothelial cells response to VEGFC, 03hr30min, biol_rep3 (MM XXII - 11)
|accession_numbers=CAGE;DRX023006;DRR025345;DRZ003770;DRZ004653;DRZ008511;DRZ009394
|sample_id=12514
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000055,UBERON:0004111,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002049,UBERON:0007798,UBERON:0001473,UBERON:0002465,UBERON:0004535,UBERON:0004536,UBERON:0006558,UBERON:0002193,UBERON:0002405,UBERON:0001009
|rna_tube_id=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002139,CL:0000213,CL:0002078,CL:0000215,CL:0000255,CL:0000115,CL:0002138
|rna_box=133
|rna_position=B3
|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=lymph node
|sample_donor(cell lot)=rep3
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=2.23000
|rna_od260/280=1.92000
|sample_cell_type=endothelial cell, lymphatic
|sample_cell_line=
|sample_collaboration=Michael Detmar (Swiss Federal Institute of Technology, ETH Zurich)
|sample_experimental_condition=Lymphatic Endothelial cells response to Vascular endothelial growth factor C
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=12.62156
|rna_concentration=0.45077
|sample_note=
|profile_hcage=CNhs13286,LSID1020,,LIBRARY SCHEDULED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000115,CL:0000144,CL:0000213,CL:0000215,CL:0000220,CL:0000222,CL:0000255,CL:0000548,CL:0002078,CL:0002138,CL:0002139,CL:0002321,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000055,UBERON:0000061,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000480,UBERON:0001009,UBERON:0001062,UBERON:0001473,UBERON:0002049,UBERON:0002193,UBERON:0002405,UBERON:0002465,UBERON:0004111,UBERON:0004535,UBERON:0004536,UBERON:0006558,UBERON:0007798
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000002,FF:0000101,FF:0000046,FF:0000001,FF:0000350,FF:0000049,FF:0000341,FF:0000356,FF:0000420
 
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|donor= biol_rep3 (MM XXII - 11)
|ffid_belonging_in_development=CL:0000222,CL:0005022
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 67: Line 40:
|fonse_treatment=EFO:0000369,FF:0000341,FF:0000420,FF:12514-133B3
|fonse_treatment=EFO:0000369,FF:0000341,FF:0000420,FF:12514-133B3
|fonse_treatment_closure=EFO:0000369,FF:0000341,FF:0000420,FF:12514-133B3
|fonse_treatment_closure=EFO:0000369,FF:0000341,FF:0000420,FF:12514-133B3
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Lymphatic%2520Endothelial%2520cells%2520response%2520to%2520VEGFC%252c%252003hr30min%252c%2520biol_rep3%2520%2528MM%2520XXII%2520-%252011%2529.CNhs13286.12514-133B3.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Lymphatic%2520Endothelial%2520cells%2520response%2520to%2520VEGFC%252c%252003hr30min%252c%2520biol_rep3%2520%2528MM%2520XXII%2520-%252011%2529.CNhs13286.12514-133B3.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Lymphatic%2520Endothelial%2520cells%2520response%2520to%2520VEGFC%252c%252003hr30min%252c%2520biol_rep3%2520%2528MM%2520XXII%2520-%252011%2529.CNhs13286.12514-133B3.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Lymphatic%2520Endothelial%2520cells%2520response%2520to%2520VEGFC%252c%252003hr30min%252c%2520biol_rep3%2520%2528MM%2520XXII%2520-%252011%2529.CNhs13286.12514-133B3.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Lymphatic%2520Endothelial%2520cells%2520response%2520to%2520VEGFC%252c%252003hr30min%252c%2520biol_rep3%2520%2528MM%2520XXII%2520-%252011%2529.CNhs13286.12514-133B3.hg38.nobarcode.ctss.bed.gz
|id=FF:12514-133B3
|is_a=EFO:0002091;;FF:0000420
|is_obsolete=
|library_id=CNhs13286
|library_id_phase_based=2:CNhs13286
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;12514
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;12514
|name=Lymphatic Endothelial cells response to VEGFC
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs13286,LSID1020,release013,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=133
|rna_catalog_number=
|rna_concentration=0.45
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=2.23
|rna_od260/280=1.92
|rna_position=B3
|rna_rin=
|rna_sample_type=
|rna_tube_id=133B3
|rna_weight_ug=12.62
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=endothelial cell, lymphatic
|sample_collaboration=Michael Detmar (Swiss Federal Institute of Technology, ETH Zurich)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=rep3
|sample_ethnicity=
|sample_experimental_condition=Lymphatic Endothelial cells response to Vascular endothelial growth factor C
|sample_id=12514
|sample_note=
|sample_sex=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=lymph node
|time= 03hr30min
|timecourse=Lymphatic_EC_response_to_VEGFC
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:12514-133B3;search_select_hide=table117:FF:12514-133B3
}}
}}

Latest revision as of 18:39, 4 June 2020


Name:Lymphatic Endothelial cells response to VEGFC
Species:Human (Homo sapiens)
Library ID:CNhs13286
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissuelymph node
dev stageNA
sexNA
ageNA
cell typeendothelial cell, lymphatic
cell lineNA
companyNA
collaborationMichael Detmar (Swiss Federal Institute of Technology, ETH Zurich)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021353
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13286 CAGE DRX023006 DRR025345
Accession ID Hg19

Library idBAMCTSS
CNhs13286 DRZ003770 DRZ004653
Accession ID Hg38

Library idBAMCTSS
CNhs13286 DRZ008511 DRZ009394
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: CNhs13286This 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: CNhs13286This 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: CNhs13286


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)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002139 (endothelial cell of vascular tree)
0000213 (lining cell)
0002078 (meso-epithelial cell)
0000215 (barrier cell)
0000255 (eukaryotic cell)
0000115 (endothelial cell)
0002138 (endothelial cell of lymphatic vessel)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000055 (vessel)
0004111 (anatomical conduit)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002049 (vasculature)
0007798 (vascular system)
0001473 (lymphatic vessel)
0002465 (lymphoid system)
0004535 (cardiovascular system)
0004536 (lymph vasculature)
0006558 (lymphatic part of lymphoid system)
0002193 (hemolymphoid system)
0002405 (immune system)
0001009 (circulatory system)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000046 (human endothelial cell sample)
0000001 (sample)
0000350 (experimentally modified sample)
0000049 (human lymphatic endothelial cell sample)
0000341 (Vegfc treatment sample)
0000356 (210 minutes sample)
0000420 (human Lymphatic Endothelial cells 3.5h after VEGFC treatment 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:0000222 (mesodermal cell)
CL:0005022 (vascular lymphangioblast)

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