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{{f5samples
{{f5samples
|id=FF:11959-126C6
|DRA_sample_Accession=CAGE@SAMD00021225
|name=Neurons - spiral ganglion, pool1
|accession_numbers=CAGE;DRX023603;DRR025998;DRZ005250;DRZ006040;DRZ009991;DRZ010655
|sample_id=11959
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000033,UBERON:0003714,UBERON:0000395,UBERON:0000479,UBERON:0004121,UBERON:0010314,UBERON:0011216,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0005162,UBERON:0000477,UBERON:0000467,UBERON:0001714,UBERON:0010313,UBERON:0001062,UBERON:0000480,UBERON:0001785,UBERON:0000122,UBERON:0003338,UBERON:0001021,UBERON:0001032,UBERON:0000045,UBERON:0010317,UBERON:0000010,UBERON:0001016,UBERON:0000153,UBERON:0007811,UBERON:0002827,UBERON:0004456,UBERON:0002105
|rna_tube_id=126C6
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000540,CL:0000003,CL:0000548,CL:0002371,CL:0002319,CL:0000393,CL:0000211,CL:0000404,CL:0000255
|rna_box=126
|rna_position=C6
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_dev_stage=
|sample_tissue=ANATOMICAL SYSTEM
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=
|sample_cell_line=
|sample_collaboration=Albert Edge (Department of Otolaryngology, Harvard Medical School)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=
|rna_weight_ug=0.25
|rna_concentration=0.004
|sample_note=
|profile_hcage=CNhs14147,LSID1176,release016,COMPLETED
|profile_cagescan=
|profile_srnaseq=
|profile_rnaseq=
|ancestors_in_cell_lineage_facet=
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|sample_description=
|ancestors_in_ff_facet=FF:0200030
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|ffid_belonging_in_development=CL:0000133,CL:0000031,CL:0000221,UBERON:0003869,UBERON:0002532,UBERON:0006601,UBERON:0005062,UBERON:0007284,UBERON:0010316
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
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|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|id=FF:11959-126C6
|is_a=FF:0200030
|is_obsolete=
|library_id=CNhs14147
|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;11959
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;11959
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Neurons%2520-%2520spiral%2520ganglion%252c%2520pool1.CNhs14147.11959-126C6.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.hCAGE/Neurons%2520-%2520spiral%2520ganglion%252c%2520pool1.CNhs14147.11959-126C6.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Neurons%2520-%2520spiral%2520ganglion%252c%2520pool1.CNhs14147.11959-126C6.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Neurons%2520-%2520spiral%2520ganglion%252c%2520pool1.CNhs14147.11959-126C6.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.hCAGE/Neurons%2520-%2520spiral%2520ganglion%252c%2520pool1.CNhs14147.11959-126C6.mm9.nobarcode.rdna.fa.gz
|name=Neurons - spiral ganglion, pool1
|namespace=
|part_of=
|profile_cagescan=
|profile_hcage=CNhs14147,LSID1176,release016,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=126
|rna_catalog_number=
|rna_concentration=0.004
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=C6
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=126C6
|rna_weight_ug=0.25
|sample_age=
|sample_category=primary cells
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=
|sample_collaboration=Albert Edge (Department of Otolaryngology, Harvard Medical School)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11959
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=ANATOMICAL SYSTEM
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11959-126C6;search_select_hide=table117:11959-126C6
}}
}}

Latest revision as of 18:30, 4 June 2020


Name:Neurons - spiral ganglion, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs14147
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueANATOMICAL SYSTEM
dev stageNA
sexNA
ageNA
cell typeNA
cell lineNA
companyNA
collaborationAlbert Edge (Department of Otolaryngology, Harvard Medical School)
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  SAMD00021225
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs14147 CAGE DRX023603 DRR025998
Accession ID Mm9

Library idBAMCTSS
CNhs14147 DRZ005250 DRZ006040
Accession ID Mm10

Library idBAMCTSS
CNhs14147 DRZ009991 DRZ010655
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

CNhs14147



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: CNhs14147This 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: CNhs14147This 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: CNhs14147


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)
0000393 (electrically responsive cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000033 (head)
0003714 (neural tissue)
0000395 (cochlear ganglion)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0005162 (multi cell component structure)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001714 (cranial ganglion)
0010313 (neural crest-derived structure)
0001062 (anatomical entity)
0000480 (anatomical group)
0001785 (cranial nerve)
0000122 (neuron projection bundle)
0003338 (ganglion of peripheral nervous system)
0001021 (nerve)
0001032 (sensory system)
0000045 (ganglion)
0010317 (germ layer / neural crest derived structure)
0000010 (peripheral nervous system)
0001016 (nervous system)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002827 (vestibulocochlear ganglion)
0004456 (entire sense organ system)
0002105 (vestibulo-auditory system)

FF: FANTOM5
0200030 (neurons - spiral ganglion 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:0000031 (neuroblast)
CL:0000221 (ectodermal cell)
UBERON:0003869 (presumptive ganglion)
UBERON:0002532 (epiblast (generic))
UBERON:0006601 (presumptive ectoderm)
UBERON:0005062 (neural fold)
UBERON:0007284 (presumptive neural plate)
UBERON:0010316 (germ layer / neural crest)

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