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{{f5samples
{{f5samples
|id=FF:13534-145G6
|DRA_sample_Accession=CAGE@SAMD00022150
|name=cerebellar granule cells, embryo E13, biol_rep3 (E13R3)
|accession_numbers=CAGE;DRX024029;DRR026434;DRZ005686;DRZ006466;DRZ010301;DRZ010959
|sample_id=13534
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000955,UBERON:0002037,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000481,UBERON:0000073,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0002680,UBERON:0002616,UBERON:0004733,UBERON:0004732,UBERON:0010317,UBERON:0001017,UBERON:0001016,UBERON:0001895,UBERON:0002028
|rna_tube_id=145G6
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000117,CL:0000393,CL:0000211,CL:0000404,CL:0000255,CL:0000120,CL:0001031
|rna_box=145
|rna_position=G6
|sample_cell_lot=E13R3
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=SPECIES
|sample_strain=
|sample_dev_stage=
|sample_tissue=
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=SELECT CELL TYPE
|sample_cell_line=
|sample_collaboration=
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=0.49
|rna_concentration=0.01
|sample_note=
|profile_hcage=CNhs14146,LSID1176,release016,COMPLETED
|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:0000102,FF:0000002,FF:0000101,FF:0000103,FF:0000001,FF:0000999,FF:0000292,FF:0000004,FF:0000293,FF:0000199
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|ffid_belonging_in_development=CL:0000133,CL:0000337,CL:0000031,CL:0000221,FF:0000294
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 39:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|id=FF:13534-145G6
|is_a=EFO:0002091;;FF:0000199;;FF:0000293
|is_obsolete=
|library_id=CNhs14146
|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;13534
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;13534
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/cerebellar%2520granule%2520cells%252c%2520embryo%2520E13%252c%2520biol_rep3%2520%2528E13R3%2529.CNhs14146.13534-145G6.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/cerebellar%2520granule%2520cells%252c%2520embryo%2520E13%252c%2520biol_rep3%2520%2528E13R3%2529.CNhs14146.13534-145G6.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/cerebellar%2520granule%2520cells%252c%2520embryo%2520E13%252c%2520biol_rep3%2520%2528E13R3%2529.CNhs14146.13534-145G6.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/cerebellar%2520granule%2520cells%252c%2520embryo%2520E13%252c%2520biol_rep3%2520%2528E13R3%2529.CNhs14146.13534-145G6.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/cerebellar%2520granule%2520cells%252c%2520embryo%2520E13%252c%2520biol_rep3%2520%2528E13R3%2529.CNhs14146.13534-145G6.mm9.nobarcode.rdna.fa.gz
|name=cerebellar granule cells, embryo E13, biol_rep3 (E13R3)
|namespace=
|part_of=
|profile_cagescan=
|profile_hcage=CNhs14146,LSID1176,release016,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=145
|rna_catalog_number=
|rna_concentration=0.01
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=G6
|rna_rin=
|rna_sample_type=
|rna_tube_id=145G6
|rna_weight_ug=0.49
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=E13R3
|sample_cell_type=SELECT CELL TYPE
|sample_collaboration=
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=13534
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:13534-145G6;search_select_hide=table117:13534-145G6
}}
}}

Latest revision as of 19:01, 4 June 2020


Name:cerebellar granule cells, embryo E13, biol_rep3 (E13R3)
Species:Mouse (Mus musculus)
Library ID:CNhs14146
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexNA
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationNA
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  SAMD00022150
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14146 CAGE DRX024029 DRR026434
Accession ID Mm9

Library idBAMCTSS
CNhs14146 DRZ005686 DRZ006466
Accession ID Mm10

Library idBAMCTSS
CNhs14146 DRZ010301 DRZ010959
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

CNhs14146



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: CNhs14146This 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: CNhs14146This 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: CNhs14146


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)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0002371 (somatic cell)
0002319 (neural cell)
0000117 (CNS neuron (sensu Vertebrata))
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000120 (granule cell)
0001031 (cerebellar granule cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000922 (embryo)
0000955 (brain)
0002037 (cerebellum)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0000481 (multi-tissue structure)
0000073 (regional part of nervous system)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0002680 (regional part of metencephalon)
0002616 (regional part of brain)
0004733 (segmental subdivision of hindbrain)
0004732 (segmental subdivision of nervous system)
0010317 (germ layer / neural crest derived structure)
0001017 (central nervous system)
0001016 (nervous system)
0001895 (metencephalon)
0002028 (hindbrain)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000999 (fetal tissue sample)
0000292 (embryonic day sample - mouse)
0000004 (tissue sample)
0000293 (mouse embryonic day 13 sample)
0000199 (cerebellar granule 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
CL:0000133 (neurectodermal cell)
CL:0000337 (neuroblast (sensu Vertebrata))
CL:0000031 (neuroblast)
CL:0000221 (ectodermal cell)
FF:0000294 (mouse embryonic day 11 sample)

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