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{{f5samples
{{f5samples
|id=FF:3715-172C2
|DRA_sample_Accession=CAGE@SAMD00022489
|name=macrophage, TB infection, stimulated BMDM+IFNg(caMph), 004hr, biol_rep3
|accession_numbers=CAGE;DRX024210;DRR026615;DRZ005867;DRZ006647;DRZ010482;DRZ011140
|sample_id=3715
|ancestors_in_anatomy_facet=
|rna_tube_id=172C2
|rna_box=172
|rna_position=C2
|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=9.8
|rna_od260/230=2
|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=20.5825
|rna_concentration=0.41165
|sample_note=
|profile_hcage=CNhs11639,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=
|ancestors_in_ff_facet=FF:0000101,FF:0000103,FF:0000001
|comment=
|created_by=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|donor= biol_rep3
|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=
Line 66: Line 39:
|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:3715-172C2
|is_a=FF:0000103
|is_obsolete=
|library_id=CNhs11639
|library_id_phase_based=2:CNhs11639
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;3715
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;3715
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/macrophage%252c%2520TB%2520infection%252c%2520stimulated%2520BMDM%252bIFNg%2528caMph%2529%252c%2520without%2520Mtb%252c%2520004hr%252c%2520biol_rep3.CNhs11639.3715-172C2.mm10.nobarcode.bam
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/macrophage%252c%2520TB%2520infection%252c%2520stimulated%2520BMDM%252bIFNg%2528caMph%2529%252c%2520without%2520Mtb%252c%2520004hr%252c%2520biol_rep3.CNhs11639.3715-172C2.mm10.nobarcode.ctss.bed.gz
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520TB%2520infection%252c%2520stimulated%2520BMDM%252bIFNg%2528caMph%2529%252c%2520without%2520Mtb%252c%2520004hr%252c%2520biol_rep3.CNhs11639.3715-172C2.mm9.nobarcode.bam
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520TB%2520infection%252c%2520stimulated%2520BMDM%252bIFNg%2528caMph%2529%252c%2520without%2520Mtb%252c%2520004hr%252c%2520biol_rep3.CNhs11639.3715-172C2.mm9.ctss.bed.gz
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520TB%2520infection%252c%2520stimulated%2520BMDM%252bIFNg%2528caMph%2529%252c%2520without%2520Mtb%252c%2520004hr%252c%2520biol_rep3.CNhs11639.3715-172C2.mm9.nobarcode.rdna.fa.gz
|name=macrophage, TB infection, stimulated BMDM+IFNg(caMph)
|namespace=
|namespace=
|part_of=
|part_of=
|profile_cagescan=
|profile_hcage=CNhs11639,LSID804,release016,COMPLETED
|profile_rnaseq=
|profile_srnaseq=
|rna_box=172
|rna_catalog_number=
|rna_concentration=0.41165
|rna_extraction_protocol=
|rna_lot_number=
|rna_od260/230=2
|rna_od260/280=2.07
|rna_position=C2
|rna_rin=9.8
|rna_sample_type=total RNA
|rna_tube_id=172C2
|rna_weight_ug=20.5825
|sample_age=
|sample_category=time courses
|sample_cell_catalog=
|sample_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=3715
|sample_note=
|sample_sex=male
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/6J
|sample_tissue=bone marrow
|time= 004hr
|timecourse=BMM_TB_activation_IFNg
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:3715-172C2;search_select_hide=table117:3715-172C2
}}
}}

Latest revision as of 19:13, 4 June 2020


Name:macrophage, TB infection, stimulated BMDM+IFNg(caMph)
Species:Mouse (Mus musculus)
Library ID:CNhs11639
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainC57BL/6J
tissuebone marrow
dev stageUNDEFINED_DEV_STAGE
sexmale
ageNA
cell typemacrophage
cell lineNA
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

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00022489
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11639 CAGE DRX024210 DRR026615
Accession ID Mm9

Library idBAMCTSS
CNhs11639 DRZ005867 DRZ006647
Accession ID Mm10

Library idBAMCTSS
CNhs11639 DRZ010482 DRZ011140
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload





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

CNhs11639



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: CNhs11639This 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: CNhs11639This 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: CNhs11639


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
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)

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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