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{{f5samples
{{f5samples
|id=FF:12215-129E1
|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
|name=Inner ear stem cells, 1st generation stem cells, pool1
|sample_id=12215
|rna_tube_id=129E1
|rna_box=129
|rna_position=E1
|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=7.2
|rna_concentration=0.289
|sample_note=
|profile_hcage=CNhs11929,LSID835,release010,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_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=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 33:
|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:12215-129E1
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000256
|is_a=EFO:0002091;;FF:0000002;;FF:0000103;;FF:0000256
|name=Inner ear stem cells, 1st generation stem cells, pool1
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs11929,LSID835,release010,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=129
|rna_catalog_number=
|rna_concentration=0.289
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=E1
|rna_rin=
|rna_sample_type=
|rna_tube_id=129E1
|rna_weight_ug=7.2
|sample_age=
|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=12215
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=organ of corti
|top_motifs=
}}
}}

Revision as of 15:07, 21 March 2012


Name:Inner ear stem cells, 1st generation stem cells, pool1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM: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
Download raw sequence, BAM & CTSS
Mm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
Mm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} donwload]





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

CNhs11929



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: CNhs11929This 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: CNhs11929This 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: CNhs11929


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)
0000006 (neuronal receptor cell)
0000031 (neuroblast)
0000034 (stem cell)
0000047 (neuronal stem cell)
0000048 (multi fate stem cell)
0000055 (non-terminally differentiated cell)
0000066 (epithelial cell)
0000098 (sensory epithelial cell)
0000133 (neurectodermal cell)
0000197 (receptor cell)
0000199 (mechanoreceptor cell)
0000202 (auditory hair cell)
0000211 (electrically active cell)
0000221 (ectodermal cell)
0000255 (eukaryotic cell)
0000393 (electrically responsive cell)
0000404 (electrically signaling cell)
0000540 (neuron)
0000548 (animal cell)
0000589 (cochlear inner hair cell)
0000723 (somatic stem cell)
0000855 (sensory hair cell)
0002319 (neural cell)
0002321 (embryonic cell)
0002371 (somatic cell)
0002374 (ear hair cell)
0002491 (auditory epithelial cell)

UBERON: Anatomy
0000020 (sense organ)
0000033 (head)
0000058 (duct)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000073 (regional part of nervous system)
0000075 (subdivision of skeletal system)
0000153 (anterior region of body)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000922 (embryo)
0000923 (germ layer)
0000924 (ectoderm)
0000926 (mesoderm)
0001016 (nervous system)
0001017 (central nervous system)
0001032 (sensory system)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0001678 (temporal bone)
0001690 (ear)
0001694 (petrous part of temporal bone)
0001703 (neurocranium)
0001839 (bony labyrinth)
0001844 (cochlea)
0001846 (internal ear)
0001849 (membranous labyrinth)
0001855 (cochlear duct of membranous labyrinth)
0002050 (embryonic structure)
0002105 (vestibulo-auditory system)
0002204 (musculoskeletal system)
0002227 (spiral organ of cochlea)
0002241 (chondrocranium)
0002329 (somite)
0002342 (neural crest)
0002346 (neurectoderm)
0002499 (cochlear labyrinth)
0002532 (epiblast (generic))
0003059 (presomitic mesoderm)
0003075 (neural plate)
0003077 (paraxial mesoderm)
0003089 (sclerotome)
0003104 (mesenchyme)
0003128 (cranium)
0003129 (skull)
0003457 (head bone)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004121 (ectoderm-derived structure)
0004288 (skeleton)
0004456 (entire sense organ system)
0004681 (vestibular system)
0004765 (skeletal element)
0004766 (cranial bone)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005744 (cranial conduit)
0006598 (presumptive structure)
0007284 (presumptive neural plate)
0008001 (irregular bone)
0008193 (pneumatized bone)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

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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