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{{f5samples
 
{{f5samples
|accession_numbers=CAGE;DRX023091;DRR025430;DRZ003855;DRZ004738
+
|DRA_sample_Accession=CAGE@SAMD00021594
 +
|accession_numbers=CAGE;DRX023091;DRR025430;DRZ003855;DRZ004738;DRZ008596;DRZ009479
 
|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_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
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|datafreeze_phase=2
 
|datafreeze_phase=2
 
|def=
 
|def=
 +
|donor= donor3 (t2 Subject3)
 
|ffid_belonging_in_development=CL:0000049,CL:0000134
 
|ffid_belonging_in_development=CL:0000049,CL:0000134
 
|fonse_cell_line=
 
|fonse_cell_line=
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|fonse_treatment_closure=EFO:0000369,FF:0000335,FF:0000567,FF:0000625,FF:12895-137H6
 
|fonse_treatment_closure=EFO:0000369,FF:0000335,FF:0000567,FF:0000625,FF:12895-137H6
 
|has_quality=
 
|has_quality=
 +
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Monocyte-derived%2520macrophages%2520response%2520to%2520LPS%252c%252000hr15min%252c%2520donor3%2520%2528t2%2520Subject3%2529.CNhs13175.12895-137H6.hg19.nobarcode.bam
 +
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Monocyte-derived%2520macrophages%2520response%2520to%2520LPS%252c%252000hr15min%252c%2520donor3%2520%2528t2%2520Subject3%2529.CNhs13175.12895-137H6.hg19.ctss.bed.gz
 +
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.timecourse.hCAGE/Monocyte-derived%2520macrophages%2520response%2520to%2520LPS%252c%252000hr15min%252c%2520donor3%2520%2528t2%2520Subject3%2529.CNhs13175.12895-137H6.hg19.nobarcode.rdna.fa.gz
 +
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Monocyte-derived%2520macrophages%2520response%2520to%2520LPS%252c%252000hr15min%252c%2520donor3%2520%2528t2%2520Subject3%2529.CNhs13175.12895-137H6.hg38.nobarcode.bam
 +
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.timecourse.hCAGE/Monocyte-derived%2520macrophages%2520response%2520to%2520LPS%252c%252000hr15min%252c%2520donor3%2520%2528t2%2520Subject3%2529.CNhs13175.12895-137H6.hg38.nobarcode.ctss.bed.gz
 
|id=FF:12895-137H6
 
|id=FF:12895-137H6
 
|is_a=EFO:0002091;;FF:0000567
 
|is_a=EFO:0002091;;FF:0000567
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|library_id=CNhs13175
 
|library_id=CNhs13175
 
|library_id_phase_based=2:CNhs13175
 
|library_id_phase_based=2:CNhs13175
|name=Monocyte-derived macrophages response to LPS, 00hr15min, donor3 (t2 Subject3)
+
|microRNAs=
 +
|microRNAs_nn=
 +
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;12895
 +
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;12895
 +
|name=Monocyte-derived macrophages response to LPS
 
|namespace=FANTOM5
 
|namespace=FANTOM5
 
|part_of=
 
|part_of=
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|sample_strain=
 
|sample_strain=
 
|sample_tissue=t2
 
|sample_tissue=t2
|timecourse=human_macrophages_response_to_LPS
+
|time= 00hr15min
 +
|timecourse=Macrophage_response_to_LPS
 
|top_motifs=
 
|top_motifs=
 
|xref=
 
|xref=
 
}}
 
}}

Latest revision as of 12:57, 10 August 2017


Name:Monocyte-derived macrophages response to LPS
Species:Human (Homo sapiens)
Library ID:CNhs13175
Sample type:time courses
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuet2
dev stageNA
sexn/a
ageadult
cell typemacrophage
cell lineNA
companyNA
collaborationKenneth Baillie (Roslin Institute)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typeRNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00021594
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13175 CAGE DRX023091 DRR025430
Accession ID Hg19

Library idBAMCTSS
CNhs13175 DRZ003855 DRZ004738
Accession ID Hg38

Library idBAMCTSS
CNhs13175 DRZ008596 DRZ009479
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
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.
Analyst:NA

link to dataset.
data
No results for this sample

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: CNhs13175This 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: CNhs13175This 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: CNhs13175


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

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
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000625 (experimental infection sample)
0000350 (experimentally modified sample)
0000345 (15 minutes sample)
0000086 (human macrophage sample)
0000335 (LPS treatment sample)
0000567 (human Monocyte-derived macrophages 15min after LPS treatment sample)

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

link to source data
data

CL:0000049 (common myeloid progenitor)
CL:0000134 (mesenchymal cell)