Personal tools

FF:3716-172D2: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{f5samples |id=FF:3716-172D2 |name=macrophage, TB infection, stimulated BMDM+IFNg(caMph), 006hr, biol_rep3 |sample_id=3716 |rna_tube_id=172D2 |rna_box=172 |rna_position=D2 |s...")
 
No edit summary
Line 1: Line 1:
{{f5samples
{{f5samples
|id=FF:3716-172D2
|ancestors_in_anatomy_facet=
|name=macrophage, TB infection, stimulated BMDM+IFNg(caMph), 006hr, biol_rep3
|sample_id=3716
|rna_tube_id=172D2
|rna_box=172
|rna_position=D2
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_dev_stage=UNDEFINED_DEV_STAGE
|sample_tissue=bone marrow
|sample_donor(cell lot)=
|sample_sex=male
|sample_age=
|sample_ethnicity=
|rna_rin=9.1
|rna_od260/230=1.93
|rna_od260/280=2.07
|sample_cell_type=macrophage
|sample_cell_line=UNDEFINED_CELL_LINE
|sample_collaboration=Frank Brombacher (University of Cape Town, South Africa)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=
|rna_weight_ug=20.9685
|rna_concentration=0.41937
|sample_note=
|profile_hcage=CNhs11640,LSID804,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=
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=
|is_a=
|id=FF:3716-172D2
|is_a=FF:0000103
|is_obsolete=
|name=macrophage, TB infection, stimulated BMDM+IFNg(caMph), 006hr, biol_rep3
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=
|profile_hcage=CNhs11640,LSID804,release016,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=172
|rna_catalog_number=
|rna_concentration=0.41937
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=1.93
|rna_od260/280=2.07
|rna_position=D2
|rna_rin=9.1
|rna_sample_type=total RNA
|rna_tube_id=172D2
|rna_weight_ug=20.9685
|sample_age=
|sample_cell_catalog=
|sample_cell_line=UNDEFINED_CELL_LINE
|sample_cell_lot=
|sample_cell_type=macrophage
|sample_collaboration=Frank Brombacher (University of Cape Town, South Africa)
|sample_company=
|sample_description=
|sample_dev_stage=UNDEFINED_DEV_STAGE
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=3716
|sample_note=
|sample_sex=male
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=bone marrow
|top_motifs=
|xref=
}}
}}

Revision as of 03:55, 28 June 2012


Name:macrophage, TB infection, stimulated BMDM+IFNg(caMph), 006hr, biol_rep3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/6J
tissuebone marrow
dev stageUNDEFINED_DEV_STAGE
sexmale
ageNA
cell typemacrophage
cell lineUNDEFINED_CELL_LINE
companyNA
collaborationFrank Brombacher (University of Cape Town, South Africa)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
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

CNhs11640



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: CNhs11640This 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: CNhs11640This 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: CNhs11640


FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
FF:0000103 mouse sample


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