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{{f5samples
{{f5samples
|id=FF:10358-105E7
|ancestors_in_anatomy_facet=
|name=substantia nigra, newborn, donor10223
|sample_id=10358
|rna_tube_id=105E7
|rna_box=105
|rna_position=E7
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=substantia nigra
|sample_donor(cell lot)=donor: 10223
|sample_sex=male
|sample_age=0
|sample_ethnicity=
|rna_rin=7.4
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_cell_line=
|sample_collaboration=Peter Heutink
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=
|rna_concentration=1.1
|sample_note=
|profile_hcage=CNhs14076,LSID1158,release016,COMPLETED
|profile_cagescan=
|profile_srnaseq=
|profile_rnaseq=
|ancestors_in_cell_lineage_facet=
|ancestors_in_cell_lineage_facet=
|ancestors_in_anatomy_facet=
|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=
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|fonse_treatment=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|is_a=
|id=FF:10358-105E7
|is_a=EFO:0001372;;FF:0000004;;FF:0000210;;UBERON:0002038;;UBERON:0007221
|is_obsolete=
|name=substantia nigra, newborn, donor10223
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=
|profile_hcage=CNhs14076,LSID1158,release016,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=105
|rna_catalog_number=
|rna_concentration=1.1
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=
|rna_od260/280=
|rna_position=E7
|rna_rin=7.4
|rna_sample_type=total RNA
|rna_tube_id=105E7
|rna_weight_ug=
|sample_age=0
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=CELL MIXTURE - tissue sample
|sample_collaboration=Peter Heutink
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=donor: 10223
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10358
|sample_note=
|sample_sex=male
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=substantia nigra
|top_motifs=
|xref=
}}
}}

Revision as of 17:16, 27 June 2012


Name:substantia nigra, newborn, donor10223
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuesubstantia nigra
dev stageNA
sexmale
age0
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyNA
collaborationPeter Heutink
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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>dataNo results for this sample

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: CNhs14076This 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: CNhs14076This 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: CNhs14076


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

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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