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{{f5samples
{{f5samples
|id=FF:12713-135F4
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002193,UBERON:0002204,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423
|name=Monocyte-derived macrophages response to LPS, 08hr, donor1 (t16 Subject1)
|sample_id=12713
|rna_tube_id=135F4
|rna_box=135
|rna_position=F4
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=
|rna_catalog_number=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=t16
|sample_donor(cell lot)=rep1
|sample_sex=n/a
|sample_age=adult
|sample_ethnicity=Caucasian
|rna_rin=
|rna_od260/230=0.96
|rna_od260/280=2.13
|sample_cell_type=macrophage
|sample_cell_line=
|sample_collaboration=Kenneth Baillie (Roslin Institute)
|sample_experimental_condition=Monocyte derived macrophages repsonse to LPS
|sample_disease=Healthy
|rna_sample_type=RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_weight_ug=12.69
|rna_concentration=0.51
|sample_note=
|profile_hcage=CNhs12927,LSID974,release012,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000040,CL:0000048,CL:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000235,CL:0000255,CL:0000548,CL:0000557,CL:0000559,CL:0000566,CL:0000576,CL:0000723,CL:0000738,CL:0000763,CL:0000766,CL:0000837,CL:0000839,CL:0000988,CL:0001012,CL:0002009,CL:0002031,CL:0002032,CL:0002087,CL:0002194,CL:0002320,CL:0002371
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000037,CL:0000040,CL:0000048,CL:0000049,CL:0000063,CL:0000134,CL:0000144,CL:0000219,CL:0000235,CL:0000255,CL:0000548,CL:0000557,CL:0000559,CL:0000566,CL:0000576,CL:0000723,CL:0000738,CL:0000763,CL:0000766,CL:0000837,CL:0000839,CL:0000988,CL:0001012,CL:0002009,CL:0002031,CL:0002032,CL:0002087,CL:0002194,CL:0002320,CL:0002371
|ancestors_in_anatomy_facet=UBERON:0000061,UBERON:0000062,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000479,UBERON:0000480,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001062,UBERON:0001434,UBERON:0001474,UBERON:0002050,UBERON:0002193,UBERON:0002204,UBERON:0002371,UBERON:0002384,UBERON:0002390,UBERON:0002405,UBERON:0002532,UBERON:0004120,UBERON:0004765,UBERON:0005423
|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=
Line 66: Line 33:
|fonse_treatment=EFO:0000369,FF:0000335,FF:0000581,FF:0000625,FF:12713-135F4
|fonse_treatment=EFO:0000369,FF:0000335,FF:0000581,FF:0000625,FF:12713-135F4
|fonse_treatment_closure=EFO:0000369,FF:0000335,FF:0000581,FF:0000625,FF:12713-135F4
|fonse_treatment_closure=EFO:0000369,FF:0000335,FF:0000581,FF:0000625,FF:12713-135F4
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:12713-135F4
|is_a=EFO:0002091;;FF:0000210;;FF:0000581
|is_a=EFO:0002091;;FF:0000210;;FF:0000581
|name=Monocyte-derived macrophages response to LPS, 08hr, donor1 (t16 Subject1)
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12927,LSID974,release012,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=135
|rna_catalog_number=
|rna_concentration=0.51
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
|rna_lot_number=
|rna_od260/230=0.96
|rna_od260/280=2.13
|rna_position=F4
|rna_rin=
|rna_sample_type=RNA
|rna_tube_id=135F4
|rna_weight_ug=12.69
|sample_age=adult
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=macrophage
|sample_collaboration=Kenneth Baillie (Roslin Institute)
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=Healthy
|sample_donor(cell lot)=rep1
|sample_ethnicity=Caucasian
|sample_experimental_condition=Monocyte derived macrophages repsonse to LPS
|sample_id=12713
|sample_note=
|sample_sex=n/a
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=t16
|top_motifs=
}}
}}

Revision as of 15:20, 21 March 2012


Name:Monocyte-derived macrophages response to LPS, 08hr, donor1 (t16 Subject1)
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuet16
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
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} 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. <br>Analyst:NA <br><br>link to dataset.<br>dataNo results for this sample

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: CNhs12927This 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: CNhs12927This 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: CNhs12927


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)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000040 (monoblast)
0000048 (multi fate stem cell)
0000049 (common myeloid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000235 (macrophage)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000557 (granulocyte monocyte progenitor cell)
0000559 (promonocyte)
0000566 (angioblastic mesenchymal cell)
0000576 (monocyte)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000763 (myeloid cell)
0000766 (myeloid leukocyte)
0000837 (hematopoietic multipotent progenitor cell)
0000839 (myeloid lineage restricted progenitor cell)
0000988 (hematopoietic cell)
0001012 (CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor)
0002009 (macrophage dendritic cell progenitor)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002194 (monopoietic cell)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000062 (organ)
0000465 (material anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000479 (tissue)
0000480 (anatomical group)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001062 (anatomical entity)
0001434 (skeletal system)
0001474 (bone element)
0002050 (embryonic structure)
0002193 (hemolymphoid system)
0002204 (musculoskeletal system)
0002371 (bone marrow)
0002384 (connective tissue)
0002390 (hematopoietic system)
0002405 (immune system)
0002532 (epiblast (generic))
0004120 (mesoderm-derived structure)
0004765 (skeletal element)
0005423 (developing anatomical structure)

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

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