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{{f5samples
{{f5samples
|id=FF:13295-142H1
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000358,UBERON:0000465,UBERON:0000468,UBERON:0000922,UBERON:0001062,UBERON:0002050,UBERON:0005423
|name=trophoblast stem cell line Rybp differentiation, day05, biol_rep1
|sample_id=13295
|rna_tube_id=142H1
|rna_box=142
|rna_position=H1
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=Rybp +d5
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_dev_stage=
|sample_tissue=
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=
|sample_ethnicity=
|rna_rin=
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=SELECT CELL TYPE
|sample_cell_line=
|sample_collaboration=Hirohiko Kodeki(RCAI)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=
|rna_extraction_protocol=
|rna_weight_ug=29.75
|rna_concentration=1.19
|sample_note=
|profile_hcage=CNhs13524,LSID1025,release012,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000144,CL:0000255,CL:0000349,CL:0000351,CL:0000548,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000144,CL:0000255,CL:0000349,CL:0000351,CL:0000548,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000358,UBERON:0000465,UBERON:0000468,UBERON:0000922,UBERON:0001062,UBERON:0002050,UBERON:0005423
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|sample_description=
|comment=
|created_by=
|creation_date=
|def=
|fonse_cell_line=FF:0000626
|fonse_cell_line=FF:0000626
|fonse_cell_line_closure=FF:0000626
|fonse_cell_line_closure=FF:0000626
Line 66: Line 33:
|fonse_treatment=EFO:0000369,FF:0000644,FF:0011206,FF:13295-142H1
|fonse_treatment=EFO:0000369,FF:0000644,FF:0011206,FF:13295-142H1
|fonse_treatment_closure=EFO:0000369,FF:0000644,FF:0011206,FF:13295-142H1
|fonse_treatment_closure=EFO:0000369,FF:0000644,FF:0011206,FF:13295-142H1
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:13295-142H1
|is_a=EFO:0002091;;FF:0000103;;FF:0011206
|is_a=EFO:0002091;;FF:0000103;;FF:0011206
|name=trophoblast stem cell line Rybp differentiation, day05, biol_rep1
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs13524,LSID1025,release012,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=142
|rna_catalog_number=
|rna_concentration=1.19
|rna_extraction_protocol=
|rna_lot_number=Rybp +d5
|rna_od260/230=
|rna_od260/280=
|rna_position=H1
|rna_rin=
|rna_sample_type=
|rna_tube_id=142H1
|rna_weight_ug=29.75
|sample_age=
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=SELECT CELL TYPE
|sample_collaboration=Hirohiko Kodeki(RCAI)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=13295
|sample_note=
|sample_sex=male
|sample_species=Mouse (Mus musculus)
|sample_strain=
|sample_tissue=
|top_motifs=
}}
}}

Revision as of 15:28, 21 March 2012


Name:trophoblast stem cell line Rybp differentiation, day05, biol_rep1
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueNA
dev stageNA
sexmale
ageNA
cell typeSELECT CELL TYPE
cell lineNA
companyNA
collaborationHirohiko Kodeki(RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberRybp +d5
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

CNhs13524



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: CNhs13524This 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: CNhs13524This 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: CNhs13524


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)
0000034 (stem cell)
0000255 (eukaryotic cell)
0000349 (extraembryonic cell)
0000351 (trophoblast cell)
0000548 (animal cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000358 (blastocyst)
0000465 (material anatomical entity)
0000468 (multi-cellular organism)
0000922 (embryo)
0001062 (anatomical entity)
0002050 (embryonic structure)
0005423 (developing anatomical structure)

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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