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{{f5samples
{{f5samples
|id=FF:12216-129E2
|DRA_sample_Accession=CAGE@SAMD00021237
|name=Inner ear stem cells, 4th generation stem cells, pool1
|accession_numbers=CAGE;DRX023619;DRR026014;DRZ005266;DRZ006056;DRZ010007;DRZ010671
|sample_id=12216
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001474,UBERON:0000033,UBERON:0000058,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0011216,UBERON:0000062,UBERON:0004111,UBERON:0000475,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000020,UBERON:0000075,UBERON:0004765,UBERON:0004766,UBERON:0008193,UBERON:0005913,UBERON:0005744,UBERON:0001032,UBERON:0003457,UBERON:0008001,UBERON:0007914,UBERON:0010317,UBERON:0002227,UBERON:0001846,UBERON:0000153,UBERON:0007811,UBERON:0002204,UBERON:0001434,UBERON:0004456,UBERON:0004339,UBERON:0002105,UBERON:0001678,UBERON:0003128,UBERON:0001694,UBERON:0004681,UBERON:0001839,UBERON:0001690,UBERON:0001844,UBERON:0001849,UBERON:0002499,UBERON:0001855,UBERON:0011137,UBERON:0010323,UBERON:0003129
|rna_tube_id=129E2
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000197,CL:0000540,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0002319,CL:0000393,CL:0000006,CL:0002374,CL:0002491,CL:0000211,CL:0000404,CL:0000255,CL:0000202,CL:0000034,CL:0000199,CL:0000098,CL:0000855,CL:0000589
|rna_box=129
|rna_position=E2
|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=organ of corti
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=hair cell, organ of corti, inner
|sample_cell_line=
|sample_collaboration=Albert Edge (Department of Otolaryngology, Harvard Medical School)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=0.70000
|rna_concentration=0.02840
|sample_note=
|profile_hcage=CNhs12544,LSID920,release012,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000006,CL:0000012,CL:0000031,CL:0000034,CL:0000047,CL:0000048,CL:0000055,CL:0000063,CL:0000066,CL:0000098,CL:0000133,CL:0000144,CL:0000197,CL:0000199,CL:0000202,CL:0000211,CL:0000220,CL:0000221,CL:0000255,CL:0000393,CL:0000404,CL:0000540,CL:0000548,CL:0000589,CL:0000723,CL:0000855,CL:0002319,CL:0002321,CL:0002371,CL:0002374,CL:0002491
|ancestors_in_anatomy_facet=UBERON:0000020,UBERON:0000032,UBERON:0000033,UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000073,UBERON:0000075,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000914,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000926,UBERON:0001016,UBERON:0001017,UBERON:0001032,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0001678,UBERON:0001690,UBERON:0001694,UBERON:0001703,UBERON:0001839,UBERON:0001844,UBERON:0001846,UBERON:0001849,UBERON:0001855,UBERON:0002050,UBERON:0002105,UBERON:0002204,UBERON:0002227,UBERON:0002241,UBERON:0002329,UBERON:0002342,UBERON:0002346,UBERON:0002499,UBERON:0002532,UBERON:0003059,UBERON:0003075,UBERON:0003077,UBERON:0003089,UBERON:0003104,UBERON:0003128,UBERON:0003129,UBERON:0003457,UBERON:0003465,UBERON:0004111,UBERON:0004120,UBERON:0004121,UBERON:0004288,UBERON:0004456,UBERON:0004681,UBERON:0004765,UBERON:0004766,UBERON:0005291,UBERON:0005423,UBERON:0005743,UBERON:0005744,UBERON:0005944,UBERON:0006598,UBERON:0007284,UBERON:0008001,UBERON:0008193,UBERON:0009142
|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:0000264,FF:0000255,FF:0000257
 
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|ffid_belonging_in_development=CL:0000133,CL:0000031,CL:0000221
|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:12216-129E2
|is_a=EFO:0002091;;FF:0000257
|is_obsolete=
|library_id=CNhs12544
|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;12216
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;12216
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/Inner%2520ear%2520stem%2520cells%252c%25204th%2520generation%2520stem%2520cells%252c%2520pool1.CNhs12544.12216-129E2.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.primary_cell.LQhCAGE/Inner%2520ear%2520stem%2520cells%252c%25204th%2520generation%2520stem%2520cells%252c%2520pool1.CNhs12544.12216-129E2.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Inner%2520ear%2520stem%2520cells%252c%25204th%2520generation%2520stem%2520cells%252c%2520pool1.CNhs12544.12216-129E2.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Inner%2520ear%2520stem%2520cells%252c%25204th%2520generation%2520stem%2520cells%252c%2520pool1.CNhs12544.12216-129E2.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.primary_cell.LQhCAGE/Inner%2520ear%2520stem%2520cells%252c%25204th%2520generation%2520stem%2520cells%252c%2520pool1.CNhs12544.12216-129E2.mm9.nobarcode.rdna.fa.gz
|name=Inner ear stem cells, 4th generation stem cells, pool1
|namespace=FANTOM5
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12544,LSID920,release012,COMPLETED
|profile_rnaseq=
|profile_srnaseq=,,,
|rna_box=129
|rna_catalog_number=
|rna_concentration=0.0284
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=E2
|rna_rin=
|rna_sample_type=
|rna_tube_id=1.29E+04
|rna_weight_ug=0.7
|sample_age=
|sample_category=primary cells
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=hair cell, organ of corti, inner
|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=12216
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=organ of corti
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:12216-129E2;search_select_hide=table117:12216-129E2
}}
}}

Latest revision as of 18:34, 4 June 2020


Name:Inner ear stem cells, 4th generation stem cells, pool1
Species:Mouse (Mus musculus)
Library ID:CNhs12544
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueorgan of corti
dev stageNA
sexNA
ageNA
cell typehair cell, organ of corti, inner
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 typeNA
extraction protocol (Details)NA

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021237
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12544 CAGE DRX023619 DRR026014
Accession ID Mm9

Library idBAMCTSS
CNhs12544 DRZ005266 DRZ006056
Accession ID Mm10

Library idBAMCTSS
CNhs12544 DRZ010007 DRZ010671
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

CNhs12544



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: CNhs12544This 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: CNhs12544This 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: CNhs12544


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)
0000197 (receptor cell)
0000540 (neuron)
0000003 (native cell)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002319 (neural cell)
0000393 (electrically responsive cell)
0000006 (neuronal receptor cell)
0002374 (ear hair cell)
0002491 (auditory epithelial cell)
0000211 (electrically active cell)
0000404 (electrically signaling cell)
0000255 (eukaryotic cell)
0000202 (auditory hair cell)
0000034 (stem cell)
0000199 (mechanoreceptor cell)
0000098 (sensory epithelial cell)
0000855 (sensory hair cell)
0000589 (cochlear inner hair cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0001474 (bone element)
0000033 (head)
0000058 (duct)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0011216 (organ system subdivision)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000020 (sense organ)
0000075 (subdivision of skeletal system)
0004765 (skeletal element)
0004766 (cranial bone)
0008193 (pneumatized bone)
0005913 (zone of bone organ)
0005744 (cranial conduit)
0001032 (sensory system)
0003457 (head bone)
0008001 (irregular bone)
0007914 (head or neck bone)
0010317 (germ layer / neural crest derived structure)
0002227 (spiral organ of cochlea)
0001846 (internal ear)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002204 (musculoskeletal system)
0001434 (skeletal system)
0004456 (entire sense organ system)
0004339 (calvarium)
0002105 (vestibulo-auditory system)
0001678 (temporal bone)
0003128 (cranium)
0001694 (petrous part of temporal bone)
0004681 (vestibular system)
0001839 (bony labyrinth)
0001690 (ear)
0001844 (cochlea)
0001849 (membranous labyrinth)
0002499 (cochlear labyrinth)
0001855 (cochlear duct of membranous labyrinth)
0011137 (axial skeletal system)
0010323 (cranial skeletal system)
0003129 (skull)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000264 (mouse inner hair cell sample)
0000255 (mouse inner hair stem cell sample)
0000257 (Inner ear stem cells (4th generation stem cells) 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)

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