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(Created page with "{{f5samples |id=FF:3705-172B1 |name=macrophage, TB infection, non-stimulated BMDM, 004hr, biol_rep3 |sample_id=3705 |rna_tube_id=172B1 |rna_box=172 |rna_position=B1 |sample_ce...")
 
 
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{{f5samples
 
{{f5samples
|id=FF:3705-172B1
+
|DRA_sample_Accession=CAGE@SAMD00022479
|name=macrophage, TB infection, non-stimulated BMDM, 004hr, biol_rep3
+
|accession_numbers=CAGE;DRX024204;DRR026609;DRZ005861;DRZ006641;DRZ010476;DRZ011134
|sample_id=3705
 
|rna_tube_id=172B1
 
|rna_box=172
 
|rna_position=B1
 
|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=9.9
 
|rna_od260/230=2.02
 
|rna_od260/280=2.08
 
|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=19.1445
 
|rna_concentration=0.38289
 
|sample_note=
 
|profile_hcage=CNhs11633,LSID804,release016,COMPLETED
 
|profile_cagescan=
 
|profile_srnaseq=
 
|profile_rnaseq=
 
|ancestors_in_cell_lineage_facet=
 
 
|ancestors_in_anatomy_facet=
 
|ancestors_in_anatomy_facet=
 +
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000988,CL:0000548,CL:0000763,CL:0002371,CL:0000766,CL:0000219,CL:0000325,CL:0000473,CL:0000234,CL:0000738,CL:0000255,CL:0000235
 
|ancestors_in_disease_facet=
 
|ancestors_in_disease_facet=
|sample_description=
+
|ancestors_in_ff_facet=FF:0000101,FF:0000103,FF:0000001,FF:0000361,FF:0200001
 +
|comment=
 +
|created_by=
 +
|creation_date=
 +
|data_phase=2
 +
|datafreeze_phase=2
 +
|def=
 +
|donor= biol_rep3
 +
|ffid_belonging_in_development=CL:0000049,CL:0000134
 
|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:3705-172B1
 +
|is_a=FF:0000103;;FF:0000361;;FF:0200001
 +
|is_obsolete=
 +
|library_id=CNhs11633
 +
|library_id_phase_based=2:CNhs11633
 +
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/mouse#cage;sample;3705
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/mouse#cage;sample;3705
 +
|mm10bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/macrophage%252c%2520TB%2520infection%252c%2520non-stimulated%2520BMDM%252c%2520without%2520Mtb%252c%2520004hr%252c%2520biol_rep3.CNhs11633.3705-172B1.mm10.nobarcode.bam
 +
|mm10ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/mm10_v2/basic/mouse.timecourse.hCAGE/macrophage%252c%2520TB%2520infection%252c%2520non-stimulated%2520BMDM%252c%2520without%2520Mtb%252c%2520004hr%252c%2520biol_rep3.CNhs11633.3705-172B1.mm10.nobarcode.ctss.bed.gz
 +
|mm9bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520TB%2520infection%252c%2520non-stimulated%2520BMDM%252c%2520without%2520Mtb%252c%2520004hr%252c%2520biol_rep3.CNhs11633.3705-172B1.mm9.nobarcode.bam
 +
|mm9ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520TB%2520infection%252c%2520non-stimulated%2520BMDM%252c%2520without%2520Mtb%252c%2520004hr%252c%2520biol_rep3.CNhs11633.3705-172B1.mm9.ctss.bed.gz
 +
|mm9fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/mouse.timecourse.hCAGE/macrophage%252c%2520TB%2520infection%252c%2520non-stimulated%2520BMDM%252c%2520without%2520Mtb%252c%2520004hr%252c%2520biol_rep3.CNhs11633.3705-172B1.mm9.nobarcode.rdna.fa.gz
 +
|name=macrophage, TB infection, non-stimulated BMDM, without Mtb
 
|namespace=
 
|namespace=
 
|part_of=
 
|part_of=
 +
|profile_cagescan=
 +
|profile_hcage=CNhs11633,LSID804,release016,COMPLETED
 +
|profile_rnaseq=
 +
|profile_srnaseq=
 +
|rna_box=172
 +
|rna_catalog_number=
 +
|rna_concentration=0.38289
 +
|rna_extraction_protocol=
 +
|rna_lot_number=
 +
|rna_od260/230=2.02
 +
|rna_od260/280=2.08
 +
|rna_position=B1
 +
|rna_rin=9.9
 +
|rna_sample_type=total RNA
 +
|rna_tube_id=172B1
 +
|rna_weight_ug=19.1445
 +
|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=3705
 +
|sample_note=
 +
|sample_sex=male
 +
|sample_species=Mouse (Mus musculus)
 +
|sample_strain=C57BL/6J
 +
|sample_tissue=bone marrow
 +
|time= 004hr
 +
|timecourse=BMM_TB_infection_control
 +
|top_motifs=
 +
|xref=
 +
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:3705-172B1;search_select_hide=table117:3705-172B1
 
}}
 
}}

Latest revision as of 10:13, 4 June 2020


Name:macrophage, TB infection, non-stimulated BMDM, without Mtb
Species:Mouse (Mus musculus)
Library ID:CNhs11633
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  SAMD00022479
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs11633 CAGE DRX024204 DRR026609
Accession ID Mm9

Library idBAMCTSS
CNhs11633 DRZ005861 DRZ006641
Accession ID Mm10

Library idBAMCTSS
CNhs11633 DRZ010476 DRZ011134
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

CNhs11633



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: CNhs11633This 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: CNhs11633This 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: CNhs11633


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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0000763 (myeloid cell)
0002371 (somatic cell)
0000766 (myeloid leukocyte)
0000219 (motile cell)
0000325 (stuff accumulating cell)
0000473 (defensive cell)
0000234 (phagocyte)
0000738 (leukocyte)
0000255 (eukaryotic cell)
0000235 (macrophage)

FF: FANTOM5
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0000361 (4 hr sample)
0200001 (macrophage, TB infection 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
CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)