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{{f5samples
{{f5samples
|id=FF:11727-123D8
|DRA_sample_Accession=CAGE@SAMD00021199
|name=
|accession_numbers=CAGE;DRX023618;DRR026013;DRZ005265;DRZ006055;DRZ010006;DRZ010670
|sample_id=11727
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0002113,UBERON:0002100,UBERON:0000062,UBERON:0000475,UBERON:0006554,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0003103,UBERON:0009569,UBERON:0000489,UBERON:0005177,UBERON:0005172,UBERON:0005173,UBERON:0011143,UBERON:0001008,UBERON:0002417,UBERON:0000916
|rna_tube_id=123D8
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000255,CL:1000497,CL:0002518
|rna_box=123
|rna_position=D8
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=Sciencell/3H
|rna_lot_number=
|rna_catalog_number=custom
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_dev_stage=
|sample_tissue=kidney
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=epithelial cell of kidney
|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
|rna_concentration=1ug/ul
|sample_note=
|profile_hcage=,,,IN_LIBRARIAN
|profile_cagescan=
|profile_srnaseq=
|profile_rnaseq=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000063,CL:0000066,CL:0000144,CL:0000255,CL:0000548,CL:0002371,CL:0002518,CL:1000497
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000480,UBERON:0000489,UBERON:0000916,UBERON:0000922,UBERON:0001008,UBERON:0001062,UBERON:0002100,UBERON:0002113,UBERON:0002417,UBERON:0003103,UBERON:0005095,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005423,UBERON:0006554,UBERON:0007687
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000115
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 38:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|id=FF:11727-123D8
|is_a=EFO:0002091;;FF:0000115
|is_obsolete=
|library_id=CNhs14555
|library_id_phase_based=2:
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;11727
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11727
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Renal%2520epithelial%2520cells%252c%2520donor1.CNhs14555.11727-123D8.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Mouse%2520Renal%2520epithelial%2520cells%252c%2520donor1.CNhs14555.11727-123D8.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Renal%2520epithelial%2520cells%252c%2520donor1.CNhs14555.11727-123D8.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Renal%2520epithelial%2520cells%252c%2520donor1.CNhs14555.11727-123D8.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Mouse%2520Renal%2520epithelial%2520cells%252c%2520donor1.CNhs14555.11727-123D8.mm9.nobarcode.rdna.fa.gz
|name=Mouse Renal epithelial cells, donor1
|namespace=FANTOM5
|part_of=
|profile_cagescan=
|profile_hcage=CNhs14555,LSID1334,,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=123
|rna_catalog_number=
|rna_concentration=0.23251
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=D8
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=123D8
|rna_weight_ug=6.27777
|sample_age=
|sample_category=primary cells
|sample_cell_catalog=
|sample_cell_line=UNDEFINED_CELL_LINE
|sample_cell_lot=
|sample_cell_type=epithelial cell of kidney
|sample_collaboration=UNDEFINED_COLLABORATION
|sample_company=
|sample_description=
|sample_dev_stage=UNDEFINED_DEV_STAGE
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=UNDEFINED_CONDITION
|sample_id=11727
|sample_note=
|sample_sex=undefined_sex_type
|sample_species=Mouse (Mus musculus)
|sample_strain=UNDEFINED_STRAIN
|sample_tissue=kidney
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11727-123D8;search_select_hide=table117:11727-123D8
}}
}}

Latest revision as of 18:16, 4 June 2020


Name:Mouse Renal epithelial cells, donor1
Species:Mouse (Mus musculus)
Library ID:CNhs14555
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainUNDEFINED_STRAIN
tissuekidney
dev stageUNDEFINED_DEV_STAGE
sexundefined_sex_type
ageNA
cell typeepithelial cell of kidney
cell lineUNDEFINED_CELL_LINE
companyNA
collaborationUNDEFINED_COLLABORATION
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  SAMD00021199
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14555 CAGE DRX023618 DRR026013
Accession ID Mm9

Library idBAMCTSS
CNhs14555 DRZ005265 DRZ006055
Accession ID Mm10

Library idBAMCTSS
CNhs14555 DRZ010006 DRZ010670
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
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>data

CNhs14555



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: CNhs14555This 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: CNhs14555This 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: CNhs14555


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)
0000255 (eukaryotic cell)
1000497 (kidney cell)
0002518 (kidney epithelial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002113 (kidney)
0002100 (trunk)
0000062 (organ)
0000475 (organism subdivision)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0003103 (compound organ)
0009569 (subdivision of trunk)
0000489 (cavitated compound organ)
0005177 (trunk region element)
0005172 (abdomen element)
0005173 (abdominal segment element)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0000916 (abdomen)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000115 (mouse kidney epithelial cell 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
NA

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