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{{f5samples
{{f5samples
|id=FF:11598-120H5
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000074,UBERON:0000080,UBERON:0000083,UBERON:0000119,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000489,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001008,UBERON:0001062,UBERON:0001225,UBERON:0001229,UBERON:0001230,UBERON:0001231,UBERON:0001285,UBERON:0001851,UBERON:0002050,UBERON:0002100,UBERON:0002113,UBERON:0002120,UBERON:0002303,UBERON:0002319,UBERON:0002321,UBERON:0002384,UBERON:0002417,UBERON:0002532,UBERON:0002553,UBERON:0003060,UBERON:0003064,UBERON:0003074,UBERON:0003081,UBERON:0003103,UBERON:0003104,UBERON:0003220,UBERON:0003567,UBERON:0003586,UBERON:0003838,UBERON:0003886,UBERON:0003887,UBERON:0003891,UBERON:0003914,UBERON:0003918,UBERON:0004111,UBERON:0004120,UBERON:0004198,UBERON:0004199,UBERON:0004208,UBERON:0004209,UBERON:0004211,UBERON:0004810,UBERON:0004819,UBERON:0004875,UBERON:0004876,UBERON:0005095,UBERON:0005103,UBERON:0005169,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005215,UBERON:0005256,UBERON:0005291,UBERON:0005423,UBERON:0005721,UBERON:0005749,UBERON:0005754,UBERON:0006553,UBERON:0006554,UBERON:0006555,UBERON:0007684,UBERON:0007687,UBERON:0009142,UBERON:0009201
|name=Renal Mesangial Cells, donor2
|sample_id=11598
|rna_tube_id=120H5
|rna_box=120
|rna_position=H5
|sample_cell_lot=N/A
|sample_cell_catalog=N/A
|sample_company=Sciencell/3H
|rna_lot_number=lot:5140
|rna_catalog_number=SC4205
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_dev_stage=
|sample_tissue=kidney
|sample_donor(cell lot)=
|sample_sex=
|sample_age=
|sample_ethnicity=
|rna_rin=9.8
|rna_od260/230=
|rna_od260/280=
|sample_cell_type=mesangial cell, intraglomerular
|sample_cell_line=
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_weight_ug=10
|rna_concentration=1.38
|sample_note=
|profile_hcage=CNhs12089,LSID839,release011,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=SRhi10013,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000066,CL:0000134,CL:0000144,CL:0000183,CL:0000219,CL:0000255,CL:0000548,CL:0000630,CL:0000650,CL:0000669,CL:0000723,CL:0002173,CL:0002320,CL:0002371,CL:0002518,CL:1000494,CL:1000497,CL:1000507
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000063,CL:0000066,CL:0000134,CL:0000144,CL:0000183,CL:0000219,CL:0000255,CL:0000548,CL:0000630,CL:0000650,CL:0000669,CL:0000723,CL:0002173,CL:0002320,CL:0002371,CL:0002518,CL:1000494,CL:1000497,CL:1000507
|ancestors_in_anatomy_facet=UBERON:0000025,UBERON:0000058,UBERON:0000061,UBERON:0000062,UBERON:0000064,UBERON:0000074,UBERON:0000080,UBERON:0000083,UBERON:0000119,UBERON:0000464,UBERON:0000465,UBERON:0000466,UBERON:0000467,UBERON:0000468,UBERON:0000475,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000481,UBERON:0000483,UBERON:0000489,UBERON:0000916,UBERON:0000922,UBERON:0000923,UBERON:0000926,UBERON:0001008,UBERON:0001062,UBERON:0001225,UBERON:0001229,UBERON:0001230,UBERON:0001231,UBERON:0001285,UBERON:0001851,UBERON:0002050,UBERON:0002100,UBERON:0002113,UBERON:0002120,UBERON:0002303,UBERON:0002319,UBERON:0002321,UBERON:0002384,UBERON:0002417,UBERON:0002532,UBERON:0002553,UBERON:0003060,UBERON:0003064,UBERON:0003074,UBERON:0003081,UBERON:0003103,UBERON:0003104,UBERON:0003220,UBERON:0003567,UBERON:0003586,UBERON:0003838,UBERON:0003886,UBERON:0003887,UBERON:0003891,UBERON:0003914,UBERON:0003918,UBERON:0004111,UBERON:0004120,UBERON:0004198,UBERON:0004199,UBERON:0004208,UBERON:0004209,UBERON:0004211,UBERON:0004810,UBERON:0004819,UBERON:0004875,UBERON:0004876,UBERON:0005095,UBERON:0005103,UBERON:0005169,UBERON:0005172,UBERON:0005173,UBERON:0005177,UBERON:0005215,UBERON:0005256,UBERON:0005291,UBERON:0005423,UBERON:0005721,UBERON:0005749,UBERON:0005754,UBERON:0006553,UBERON:0006554,UBERON:0006555,UBERON:0007684,UBERON:0007687,UBERON:0009142,UBERON:0009201
|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=
|fonse_treatment=
|fonse_treatment_closure=
|fonse_treatment_closure=
|top_motifs=
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:11598-120H5
|is_a=EFO:0002091;;FF:0000002;;FF:0000154;;FF:0000210
|is_a=EFO:0002091;;FF:0000002;;FF:0000154;;FF:0000210
|name=Renal Mesangial Cells, donor2
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12089,LSID839,release011,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=SRhi10013,,,
|rna_box=120
|rna_catalog_number=SC4205
|rna_concentration=1.38
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0
|rna_lot_number=lot:5140
|rna_od260/230=
|rna_od260/280=
|rna_position=H5
|rna_rin=9.8
|rna_sample_type=total RNA
|rna_tube_id=120H5
|rna_weight_ug=10
|sample_age=
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_lot=N/A
|sample_cell_type=mesangial cell, intraglomerular
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
|sample_company=Sciencell/3H
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11598
|sample_note=
|sample_sex=
|sample_species=Human (Homo sapiens)
|sample_strain=
|sample_tissue=kidney
|top_motifs=
}}
}}

Revision as of 14:58, 21 March 2012


Name:Renal Mesangial Cells, donor2
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuekidney
dev stageNA
sexNA
ageNA
cell typemesangial cell, intraglomerular
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberlot:5140
catalog numberSC4205
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-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: CNhs12089This 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: CNhs12089This 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: CNhs12089


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)
0000048 (multi fate stem cell)
0000066 (epithelial cell)
0000134 (mesenchymal cell)
0000183 (contractile cell)
0000219 (motile cell)
0000255 (eukaryotic cell)
0000548 (animal cell)
0000630 (supportive cell)
0000650 (mesangial cell)
0000669 (pericyte cell)
0000723 (somatic stem cell)
0002173 (extraglomerular mesangial cell)
0002320 (connective tissue cell)
0002371 (somatic cell)
0002518 (kidney epithelial cell)
1000494 (nephron tubule epithelial cell)
1000497 (kidney cell)
1000507 (kidney tubule cell)

UBERON: Anatomy
0000025 (tube)
0000058 (duct)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000074 (renal glomerulus)
0000080 (mesonephros)
0000083 (mesonephric tubule)
0000119 (cell layer)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000477 (anatomical cluster)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000483 (epithelium)
0000489 (cavitated compound organ)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000926 (mesoderm)
0001008 (renal system)
0001062 (anatomical entity)
0001225 (cortex of kidney)
0001229 (renal corpuscle)
0001230 (glomerular capsule)
0001231 (nephron tubule)
0001285 (nephron)
0001851 (cortex)
0002050 (embryonic structure)
0002100 (trunk)
0002113 (kidney)
0002120 (pronephros)
0002303 (juxtaglomerular apparatus)
0002319 (mesangium)
0002321 (extraglomerular mesangium)
0002384 (connective tissue)
0002417 (abdominal segment of trunk)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003060 (pronephric duct)
0003064 (intermediate mesoderm)
0003074 (mesonephric duct)
0003081 (lateral plate mesoderm)
0003103 (compound organ)
0003104 (mesenchyme)
0003220 (metanephric mesenchyme)
0003567 (abdomen connective tissue)
0003586 (trunk connective tissue)
0003838 (abdominal segment connective tissue)
0003886 (body cavity precursor)
0003887 (intraembryonic coelom)
0003891 (stroma)
0003914 (epithelial tube)
0003918 (kidney mesenchyme)
0004111 (anatomical conduit)
0004120 (mesoderm-derived structure)
0004198 (comma-shaped body)
0004199 (S-shaped body)
0004208 (nephrogenic mesenchyme)
0004209 (renal vesicle)
0004211 (nephron epithelium)
0004810 (nephron tubule epithelium)
0004819 (kidney epithelium)
0004875 (nephrogenic cord)
0004876 (urogenital ridge)
0005095 (kidney rudiment)
0005103 (mesonephric epithelium)
0005169 (interstitial tissue)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005215 (kidney interstitium)
0005256 (trunk mesenchyme)
0005291 (embryonic tissue)
0005423 (developing anatomical structure)
0005721 (pronephric mesoderm)
0005749 (glomerular tuft)
0005754 (rostral part of nephrogenic cord)
0006553 (renal duct)
0006554 (urinary system structure)
0006555 (excretory tube)
0007684 (uriniferous tubule)
0007687 (kidney field)
0009142 (entire embryonic mesenchyme)
0009201 (nephric duct)

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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