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{{f5samples
{{f5samples
|id=FF:10120-102F3
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001895,UBERON:0002028,UBERON:0002037,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0002616,UBERON:0002680,UBERON:0003057,UBERON:0003075,UBERON:0003076,UBERON:0004121,UBERON:0004732,UBERON:0004733,UBERON:0005068,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007135,UBERON:0007284
|name=cerebellum, embryo E17, biol_rep1 (E17R1)
|sample_id=10120
|rna_tube_id=102F3
|rna_box=102
|rna_position=F3
|sample_cell_lot=
|sample_cell_catalog=NA
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_dev_stage=17 days embryo
|sample_tissue=cerebellum
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=9.8
|rna_od260/230=1.64
|rna_od260/280=1.91
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=Dan Goldowitz(University of British Columbia Canada)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=63.9
|rna_concentration=0.71
|sample_note=
|profile_hcage=CNhs12818,LSID972,release012,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000033,UBERON:0000061,UBERON:0000062,UBERON:0000063,UBERON:0000064,UBERON:0000073,UBERON:0000153,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000922,UBERON:0000923,UBERON:0000924,UBERON:0000955,UBERON:0001016,UBERON:0001017,UBERON:0001049,UBERON:0001062,UBERON:0001895,UBERON:0002028,UBERON:0002037,UBERON:0002050,UBERON:0002346,UBERON:0002532,UBERON:0002616,UBERON:0002680,UBERON:0003057,UBERON:0003075,UBERON:0003076,UBERON:0004121,UBERON:0004732,UBERON:0004733,UBERON:0005068,UBERON:0005423,UBERON:0005743,UBERON:0006598,UBERON:0007135,UBERON:0007284
|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:10120-102F3
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011188
|is_a=EFO:0002091;;FF:0000004;;FF:0000103;;FF:0011188
|name=cerebellum, embryo E17, biol_rep1 (E17R1)
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12818,LSID972,release012,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=102
|rna_catalog_number=
|rna_concentration=0.71
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=1.64
|rna_od260/280=1.91
|rna_position=F3
|rna_rin=9.8
|rna_sample_type=
|rna_tube_id=102F3
|rna_weight_ug=63.9
|sample_age=
|sample_cell_catalog=NA
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=Dan Goldowitz(University of British Columbia Canada)
|sample_company=
|sample_description=
|sample_dev_stage=17 days embryo
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10120
|sample_note=
|sample_sex=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=cerebellum
|top_motifs=
}}
}}

Revision as of 14:02, 21 March 2012


Name:cerebellum, embryo E17, biol_rep1 (E17R1)
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuecerebellum
dev stage17 days embryo
sexNA
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationDan Goldowitz(University of British Columbia Canada)
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

CNhs12818



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: CNhs12818This 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: CNhs12818This 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: CNhs12818


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

UBERON: Anatomy
0000025 (tube)
0000033 (head)
0000061 (anatomical structure)
0000062 (organ)
0000063 (organ segment)
0000064 (organ part)
0000073 (regional part of nervous 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)
0000955 (brain)
0001016 (nervous system)
0001017 (central nervous system)
0001049 (neural tube)
0001062 (anatomical entity)
0001895 (metencephalon)
0002028 (hindbrain)
0002037 (cerebellum)
0002050 (embryonic structure)
0002346 (neurectoderm)
0002532 (epiblast (generic))
0002616 (regional part of brain)
0002680 (regional part of metencephalon)
0003057 (chordal neural plate)
0003075 (neural plate)
0003076 (posterior neural tube)
0004121 (ectoderm-derived structure)
0004732 (segmental subdivision of nervous system)
0004733 (segmental subdivision of hindbrain)
0005068 (neural rod)
0005423 (developing anatomical structure)
0006598 (presumptive structure)
0007135 (neural keel)
0007284 (presumptive neural plate)

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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