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|library_id_phase_based=1:CNhs12089
|name=Renal Mesangial Cells, donor2
|name=Renal Mesangial Cells, donor2
|namespace=FANTOM5
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Revision as of 11:28, 17 June 2014


Name:Renal Mesangial Cells, donor2
Species:Human (Homo sapiens)
Library ID:CNhs12089
Sample type:primary cells
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

CAGE Accession numbers
MethodSample accession id
CAGE  DRS008327
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12089 CAGE DRX008435 DRR009307
Accession ID Hg19

Library idBAMCTSS
CNhs12089 DRZ000732 DRZ002117
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)
0000988 (hematopoietic cell)
0000548 (animal cell)
0002320 (connective tissue cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000183 (contractile cell)
0000630 (supportive cell)
0000255 (eukaryotic cell)
0000669 (pericyte cell)
0000650 (mesangial cell)
1000500 (kidney interstitial cell)
1000618 (juxtaglomerular complex cell)
1001318 (renal interstitial pericyte)
1000746 (glomerular cell)
1000497 (kidney cell)
0002518 (kidney epithelial cell)
0002681 (kidney cortical cell)
1000449 (epithelial cell of nephron)
1000507 (kidney tubule cell)
0002584 (renal cortical epithelial cell)
1000494 (nephron tubule epithelial cell)
1000612 (kidney corpuscule cell)
0002173 (extraglomerular mesangial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002113 (kidney)
0002100 (trunk)
0000483 (epithelium)
0001851 (cortex)
0002384 (connective tissue)
0000479 (tissue)
0000064 (organ part)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
0004120 (mesoderm-derived structure)
0006555 (excretory tube)
0006554 (urinary system structure)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0003914 (epithelial tube)
0000025 (tube)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0003103 (compound organ)
0009569 (subdivision of trunk)
0004211 (nephron epithelium)
0009773 (renal tubule)
0000489 (cavitated compound organ)
0000353 (parenchyma)
0005177 (trunk region element)
0003891 (stroma)
0005172 (abdomen element)
0003567 (abdomen connective tissue)
0003838 (abdominal segment connective tissue)
0003586 (trunk connective tissue)
0010317 (germ layer / neural crest derived structure)
0001231 (nephron tubule)
0004819 (kidney epithelium)
0005173 (abdominal segment element)
0005169 (interstitial tissue)
0004810 (nephron tubule epithelium)
0001285 (nephron)
0002321 (extraglomerular mesangium)
0000074 (renal glomerulus)
0001225 (cortex of kidney)
0005215 (kidney interstitium)
0001229 (renal corpuscle)
0002303 (juxtaglomerular apparatus)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0008987 (renal parenchyma)
0007684 (uriniferous tubule)
0000916 (abdomen)
0002319 (mesangium)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000154 (human renal mesangial cell 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:0000134 (mesenchymal cell)

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