Difference between revisions of "FF:3653-171D3"
From FANTOM5_SSTAR
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|ancestors_in_cell_lineage_facet= | |ancestors_in_cell_lineage_facet= | ||
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|ancestors_in_disease_facet= | |ancestors_in_disease_facet= | ||
| − | | | + | |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= | ||
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|has_quality= | |has_quality= | ||
| − | |is_a= | + | |id=FF:3653-171D3 |
| + | |is_a=FF:0000103;;FF:0000373;;FF:0200001 | ||
| + | |name=macrophage, TB infection, stimulated BMDM+IL-13(aaMph) (without Mtb 0h), 024hr, biol_rep2 | ||
|namespace= | |namespace= | ||
|part_of= | |part_of= | ||
| + | |profile_cagescan= | ||
| + | |profile_hcage=CNhs11556,LSID788,release014,COMPLETED | ||
| + | |profile_rnaseq= | ||
| + | |profile_srnaseq= | ||
| + | |rna_box=171 | ||
| + | |rna_catalog_number= | ||
| + | |rna_concentration=0.77377 | ||
| + | |rna_extraction_protocol= | ||
| + | |rna_lot_number= | ||
| + | |rna_od260/230=2.09 | ||
| + | |rna_od260/280=2.12 | ||
| + | |rna_position=D3 | ||
| + | |rna_rin=10 | ||
| + | |rna_sample_type=total RNA | ||
| + | |rna_tube_id=171D3 | ||
| + | |rna_weight_ug=38.6885 | ||
| + | |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=3653 | ||
| + | |sample_note= | ||
| + | |sample_sex=male | ||
| + | |sample_species=Mouse (Mus musculus) | ||
| + | |sample_strain=BALB/c | ||
| + | |sample_tissue=bone marrow | ||
| + | |top_motifs= | ||
}} | }} | ||
Revision as of 06:34, 21 March 2012
| Name: | macrophage, TB infection, stimulated BMDM+IL-13(aaMph) (without Mtb 0h), 024hr, biol_rep2 |
|---|---|
| Species: | Mouse (Mus musculus) |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | UCSC |
| CAGEd-oPOSSUM: | link |
| Additional information | ||||||||||||||||||||||||||||
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Sample information
RNA information
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| Download raw sequence, BAM & CTSS | ||||||||||||
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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
CNhs11556
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: CNhs11556This 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: CNhs11556This 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: CNhs11556
FANTOM5 (FF) ontology
Direct parent terms
is_a relathionship
FF:0000103 mouse sample
FF:0000373 24 hr sample
FF:0200001 macrophage, TB infection 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
