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(Created page with "{{f5samples |id=FF:3672-171E5 |name=macrophage, TB infection, stimulated BMDM+IL-4(aaMph), 012hr, biol_rep2 |sample_id=3672 |rna_tube_id=171E5 |rna_box=171 |rna_position=E5 |s...")
 
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{{f5samples
 
{{f5samples
|id=FF:3672-171E5
+
|ancestors_in_anatomy_facet=
|name=macrophage, TB infection, stimulated BMDM+IL-4(aaMph), 012hr, biol_rep2
 
|sample_id=3672
 
|rna_tube_id=171E5
 
|rna_box=171
 
|rna_position=E5
 
|sample_cell_lot=
 
|sample_cell_catalog=
 
|sample_company=
 
|rna_lot_number=
 
|rna_catalog_number=
 
|sample_species=Mouse (Mus musculus)
 
|sample_strain=BALB/c
 
|sample_dev_stage=UNDEFINED_DEV_STAGE
 
|sample_tissue=bone marrow
 
|sample_donor(cell lot)=
 
|sample_sex=male
 
|sample_age=
 
|sample_ethnicity=
 
|rna_rin=10
 
|rna_od260/230=2.21
 
|rna_od260/280=2.13
 
|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=57.808
 
|rna_concentration=1.15616
 
|sample_note=
 
|profile_hcage=CNhs11575,LSID788,release014,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:3672-171E5
 +
|is_a=FF:0000103;;FF:0000367;;FF:0200001
 +
|name=macrophage, TB infection, stimulated BMDM+IL-4(aaMph), 012hr, biol_rep2
 
|namespace=
 
|namespace=
 
|part_of=
 
|part_of=
 +
|profile_cagescan=
 +
|profile_hcage=CNhs11575,LSID788,release014,COMPLETED
 +
|profile_rnaseq=
 +
|profile_srnaseq=
 +
|rna_box=171
 +
|rna_catalog_number=
 +
|rna_concentration=1.15616
 +
|rna_extraction_protocol=
 +
|rna_lot_number=
 +
|rna_od260/230=2.21
 +
|rna_od260/280=2.13
 +
|rna_position=E5
 +
|rna_rin=10
 +
|rna_sample_type=total RNA
 +
|rna_tube_id=171E5
 +
|rna_weight_ug=57.808
 +
|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=3672
 +
|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-4(aaMph), 012hr, biol_rep2
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainBALB/c
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.
Analyst:NA

link to dataset.
data

CNhs11575



Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.
Analyst:NA

link to dataset.
data
no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifsSummary:Association of JASPAR motif to the promoter expression in this sample. Pearson's correlation between the number of TFBSs estimated by using the position-weight matrix for each promoter and its expression is expressed as Z-score by taking the ones based on random position-weight matrix, and the tail probability of the normal distribution corresponding to the Z-score is taken as the resulting P-value. Lower P-value indicates more (non-random) association of the motif to promoter expression
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11575This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifsSummary: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 in 169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above
Analyst: Michiel de Hoon


link to dataset.
data

library id: CNhs11575This sample isn't target for the analysis

de novo motifs identified by HOMER in promoters active in this sampleSummary:The result of HOMER in this sample is shown.
Analyst:NA
library id: CNhs11575


FANTOM5 (FF) ontology


Direct parent terms


Ancestor terms (non development)Summary:Connected ontology terms with is_a, part_of or located_in relationship
Analyst: Hideya Kawaji

link to source data
data

FF: FANTOM5
NA

Ancestor terms (development)Summary:Connected ontology terms with develops_from, derives_from or preceded_by relationship
Analyst: Hideya Kawaji

link to source data
data

NA