FF:11515-119H3: Difference between revisions

Revision as of 18:37, 27 November 2014

Name:	"Renal Proximal Tubular Epithelial Cell, donor1"
Species:	Human (Homo sapiens)
Library ID:	CNhs11330
Sample type:	primary cells
Genomic View:	UCSC
CAGEd-oPOSSUM:	link

Additional information

Sample information

strain	NA
tissue	kidney
dev stage	NA
sex	NA
age	NA
cell type	"epithelial cell of kidney, proximal tubule"
cell line	NA
company	Sciencell/3H
collaboration	FANTOM5 OSC CORE (contact: Al Forrest)
External link for information	[{{{sample_info_link}}} {{{sample_info_link}}}]

RNA information

lot number	lot:5127
catalog number	SC4105
sample type	total RNA
extraction protocol (Details)	OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0

CAGE Accession numbers

Method		Sample accession id
CAGE		SAMD00005391

Library accession numbers

Library id		Method		Exp. accession id		Run accession id
CNhs11330		CAGE		DRX008437		DRR009309

Accession ID Hg19

Library id		BAM		CTSS
CNhs11330		DRZ000734		DRZ002119

Download raw sequence, BAM & CTSS

Hg19

BAM	CTSS
[{{{hg19bam}}} download]	[{{{hg19ctss}}} donwload]

Hg38

BAM	CTSS
[{{{hg38bam}}} download]	[{{{hg38ctss}}} donwload]

Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.

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. dataNo results for this sample

Repeat families with enriched expression in this sampleSummary:Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed. Analyst:NA link to dataset. data

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 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 Analyst: Michiel de Hoon link to dataset. data
library id: "CNhs11330This 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 in169 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: "CNhs11330This 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: "CNhs11330

FANTOM5 (FF) ontology

Direct parent terms

is_a relathionship
EFO:0002091 biological replicate
FF:0000155 human renal proximal tubular epithelial cell sample

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)
0000548 (animal cell)
0000075 (columnar/cuboidal epithelial cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0002078 (meso-epithelial cell)
0000255 (eukaryotic cell)
0000239 (brush border epithelial cell)
1000615 (kidney cortex tubule 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)
0002306 (epithelial cell of proximal tubule)

UBERON: Anatomy
0000468 (multi-cellular organism)
0002113 (kidney)
0002100 (trunk)
0000483 (epithelium)
0001851 (cortex)
0000479 (tissue)
0000064 (organ part)
0000062 (organ)
0004111 (anatomical conduit)
0000475 (organism subdivision)
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)
0005172 (abdomen element)
0006853 (renal cortex tubule)
0001231 (nephron tubule)
0004819 (kidney epithelium)
0005173 (abdominal segment element)
0007685 (region of nephron tubule)
0004810 (nephron tubule epithelium)
0001285 (nephron)
0004134 (proximal tubule)
0001225 (cortex of kidney)
0011143 (upper urinary tract)
0001008 (renal system)
0002417 (abdominal segment of trunk)
0008987 (renal parenchyma)
0007684 (uriniferous tubule)
0000916 (abdomen)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000151 (human renal epithelial cell sample)
0000155 (human renal proximal tubular epithelial cell 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:0000222 (mesodermal cell)

@@ Line 9: / Line 9: @@
 |created_by=
 |creation_date=
-|data_phase=1
+|data_phase=2
-|datafreeze_phase=1
+|datafreeze_phase=2
 |def=
 |expression_enrichment_score=chr2:114036488..114036504,-!p1@PAX8!2.07!117.24!PAX8;;chr17:36105042..36105060,-!p1@HNF1B!1.93!84.87!HNF1B;;chr1:201979703..201979721,+!p2@ELF3!1.89!76.46!ELF3;;chr1:201979743..201979762,+!p1@ELF3!1.88!75.44!ELF3;;chr1:209979467..209979494,-!p1@IRF6!1.61!44.09!IRF6;;chr6:50786591..50786614,+!p1@TFAP2B!1.55!34.66!TFAP2B;;chr17:46622205..46622218,-!p3@HOXB2!1.50!34.92!HOXB2;;chr17:46703687..46703740,-!p1@HOXB9!1.50!30.33!HOXB9;;chr6:34204921..34204939,+!p3@HMGA1!1.41!708.05!HMGA1;;chr17:46682321..46682362,-!p1@HOXB6!1.40!23.96!HOXB6;;chr2:122042770..122042785,-!p1@TFCP2L1!1.38!23.19!TFCP2L1;;chr17:46675558..46675577,-!p2@HOXB6!1.38!22.94!HOXB6;;chr7:27205136..27205164,-!p1@HOXA9!1.37!22.68!HOXA9;;chr2:105470562..105470582,+!p@chr2:105470562..105470582,+!1.32!19.88!POU3F3;;chr21:38071430..38071456,+!p1@SIM2!1.29!18.35!SIM2;;chr6:10415276..10415341,-!p2@TFAP2A!1.27!21.66!TFAP2A;;chr11:34642612..34642646,+!p1@EHF!1.26!17.08!EHF;;chr3:111314186..111314204,-!p1@ZBED2!1.22!15.55!ZBED2;;chr17:46622440..46622477,-!p5@HOXB2!1.18!15.80!HOXB2;;chr5:2751762..2751784,-!p1@IRX2!1.17!13.76!IRX2;;chr2:176994408..176994492,+!p1@HOXD8!1.17!13.76!HOXD8;;chr7:27205106..27205134,-!p2@HOXA9!1.16!13.51!HOXA9;;chr2:177053386..177053402,+!p1@HOXD1!1.14!12.74!HOXD1;;chr6:34204672..34204692,+!p1@HMGA1!1.06!1171.16!HMGA1;;chr2:46524897..46524911,+!p2@EPAS1!1.02!27.02!EPAS1;;chr17:46687959..46688007,-!p2@HOXB7!1.02!13.25!HOXB7;;chr17:46690839..46690884,-!p1@HOXB8!1.01!9.18!HOXB8;;chr20:42295745..42295765,+!p1@MYBL2!0.99!146.04!MYBL2;;chr17:46622229..46622257,-!p6@HOXB2!0.98!10.20!HOXB2;;chr17:46622070..46622109,-!p1@HOXB2!0.96!18.35!HOXB2;;chr17:46667594..46667619,-!p1@HOXB3!0.96!8.16!HOXB3;;chr1:24645832..24645853,+!p1@GRHL3!0.96!8.16!GRHL3;;chr7:27153454..27153469,-!p2@HOXA3!0.95!7.90!HOXA3;;chr17:46688334..46688385,-!p1@HOXB7!0.94!11.21!HOXB7;;chr17:46675420..46675465,-!p3@HOXB6!0.94!8.92!HOXB6;;chr17:7493405..7493419,-!p1@SOX15!0.94!7.65!SOX15;;chr6:10415484..10415508,-!p3@TFAP2A!0.94!7.65!TFAP2A;;chr11:65686732..65686756,+!p2@DRAP1!0.92!32.11!DRAP1;;chr15:83953397..83953425,-!p1@BNC1!0.92!8.41!BNC1;;chr10:8096631..8096660,+!p1@GATA3!0.91!8.67!GATA3;;chr6:1312325..1312340,+!p1@FOXQ1!0.90!11.72!FOXQ1;;chr20:42295713..42295738,+!p2@MYBL2!0.89!42.05!MYBL2;;chr11:65667846..65667868,-!p1@FOSL1!0.87!180.96!FOSL1;;chr2:105470536..105470556,+!p@chr2:105470536..105470556,+!0.87!6.37!POU3F3;;chr17:41623692..41623715,-!p1@ETV4!0.85!27.78!ETV4;;chr17:46703826..46703845,-!p3@HOXB9!0.85!6.12!HOXB9;;chr7:27219849..27219867,-!p6@HOXA10!0.85!6.12!HOXA10;;chr7:27224795..27224840,-!p2@HOXA11!0.84!5.86!HOXA11;;chr12:54380404..54380433,+!p3@HOXC10!0.84!5.86!HOXC10;;chr17:46703528..46703549,-!p5@HOXB9!0.84!5.86!HOXB9;;chr17:46675539..46675551,-!p7@HOXB6!0.82!5.61!HOXB6;;chr6:50789717..50789729,+!p4@TFAP2B!0.82!5.61!TFAP2B;;chr12:54393880..54393962,+!p1@HOXC9!0.82!5.61!HOXC9;;chr11:65686802..65686818,+!p6@DRAP1!0.81!9.94!DRAP1;;chr10:119303078..119303169,+!p2@EMX2!0.80!5.35!EMX2;;chr1:209979411..209979433,-!p2@IRF6!0.80!5.35!IRF6;;chr7:27192185..27192209,-!p1@HOXA3!0.80!5.35!HOXA3;;chr7:27196217..27196246,-!p2@HOXA7!0.80!5.35!HOXA7;;chr20:31350184..31350200,+!p1@DNMT3B!0.79!11.47!DNMT3B;;chr10:102505493..102505546,+!p2@PAX2!0.79!5.10!PAX2;;chr17:36105074..36105086,-!p2@HNF1B!0.79!5.10!HNF1B;;chr12:66218255..66218304,+!p3@HMGA2!0.78!14.53!HMGA2;;chr12:3069037..3069119,+!p2@TEAD4!0.77!18.35!TEAD4;;chr3:69915385..69915438,+!p3@MITF!0.77!4.84!MITF;;chr7:27224842..27224872,-!p1@HOXA11!0.77!4.84!HOXA11;;chr7:28448965..28448994,+!p2@CREB5!0.76!18.35!CREB5;;chr17:70117153..70117174,+!p1@SOX9!0.75!53.27!SOX9;;chr11:61520075..61520136,+!p1@C11orf9!0.75!10.45!C11orf9;;chr12:54410664..54410684,+!p1@HOXC4,p1@HOXC5,p1@HOXC6!0.75!4.59!HOXC5;;chr17:46675619..46675642,-!p5@HOXB6!0.75!4.59!HOXB6;;chr17:46692624..46692659,-!p3@HOXB8!0.75!4.59!HOXB8;;chr1:6479968..6479986,-!p1@HES2!0.75!4.59!HES2;;chr3:69811858..69811881,+!p5@MITF!0.75!4.59!MITF;;chr2:46524878..46524891,+!p3@EPAS1!0.74!8.41!EPAS1;;chr2:177016336..177016350,+!p1@HOXD4!0.73!4.33!HOXD4;;chr3:69811882..69811898,+!p6@MITF!0.73!4.33!MITF;;chr17:46675586..46675600,-!p6@HOXB6!0.73!4.33!HOXB6;;chr13:73633131..73633149,+!p1@KLF5!0.72!51.23!KLF5;;chr11:65668011..65668020,-!p3@FOSL1!0.71!4.08!FOSL1;;chr17:35294075..35294102,+!p1@ENST00000559335!0.71!4.08!LHX1;;chr17:45928443..45928473,-!p2@SP6!0.71!4.08!SP6;;chr17:46622175..46622186,-!p12@HOXB2!0.71!4.08!HOXB2;;chr17:46692457..46692484,-!p2@HOXB8!0.71!4.08!HOXB8;;chr7:27219833..27219845,-!p7@HOXA10!0.71!4.08!HOXA10;;chr17:46621101..46621143,-!p7@HOXB2!0.70!5.61!HOXB2;;chr6:31126291..31126399,+!p1@TCF19!0.69!41.80!TCF19;;chr17:46655704..46655718,-!p2@HOXB4!0.69!6.12!HOXB4;;chr12:66218003..66218018,+!p9@HMGA2!0.69!4.84!HMGA2;;chr7:26191809..26191890,+!p1@NFE2L3!0.67!20.90!NFE2L3;;chr12:66218598..66218645,+!p2@HMGA2!0.67!19.12!HMGA2;;chr6:10412600..10412637,-!p1@TFAP2A!0.67!6.63!TFAP2A;;chr10:8100691..8100732,+!p5@GATA3!0.66!3.57!GATA3;;chr16:51185318..51185348,-!p2@SALL1!0.66!3.57!SALL1;;chr17:46667628..46667642,-!p2@HOXB3!0.66!3.57!HOXB3;;chr21:38071403..38071428,+!p2@SIM2!0.66!3.57!SIM2;;chr6:21593973..21593988,+!p1@SOX4!0.64!142.48!SOX4;;chr6:21597765..21597779,+!p2@SOX4!0.63!31.35!SOX4;;chr12:7079780..7079791,-!p2@PHB2!0.63!19.88!PHB2;;chr7:27169801..27169844,-!p2@HOXA4!0.63!3.31!HOXA4;;chr7:97840743..97840786,+!p1@BHLHA15!0.63!3.31!BHLHA15;;chr8:102504651..102504683,+!p1@GRHL2!0.63!3.31!GRHL2;;chr2:176987441..176987454,+!p1@HOXD9!0.63!3.31!HOXD9;;chr2:96012397..96012417,+!p3@KCNIP3!0.63!3.31!KCNIP3;;chr3:111314230..111314241,-!p2@ZBED2!0.63!3.31!ZBED2;;chr19:53496768..53496799,-!p1@ZNF702P!0.62!5.35!ZNF702P;;chr17:41623009..41623053,-!p4@ETV4!0.61!5.35!ETV4;;chr17:46622114..46622138,-!p4@HOXB2!0.61!5.10!HOXB2;;chr12:66218212..66218244,+!p5@HMGA2!0.61!4.84!HMGA2;;chr11:65554528..65554546,+!p1@OVOL1!0.61!3.06!OVOL1;;chr16:51185172..51185197,-!p1@SALL1!0.61!3.06!SALL1;;chr17:46675469..46675481,-!p4@HOXB6!0.61!3.06!HOXB6;;chr17:46687935..46687950,-!p3@HOXB7!0.61!3.06!HOXB7;;chr17:46692318..46692362,-!p5@HOXB8!0.61!3.06!HOXB8;;chr17:46703212..46703238,-!p2@HOXB9!0.61!3.06!HOXB9;;chr2:176972000..176972025,+!p4@HOXD11!0.61!3.06!HOXD11;;chr2:96012353..96012378,+!p4@KCNIP3!0.61!3.06!KCNIP3;;chr4:299227..299272,-!p1@ZNF732!0.61!3.06!ZNF732;;chr6:1612300..1612324,+!p3@FOXC1!0.61!3.06!FOXC1;;chr7:27196267..27196311,-!p1@HOXA7!0.61!3.06!HOXA7;;chr1:24646002..24646013,+!p3@GRHL3!0.61!3.06!GRHL3;;chr10:104155480..104155534,+!p2@NFKB2!0.60!23.19!NFKB2;;chr17:41622925..41622976,-!p3@ETV4!0.60!4.84!ETV4;;chr12:66218836..66218888,+!p1@HMGA2!0.59!32.62!HMGA2;;chr20:50159198..50159299,-!p1@NFATC2!0.59!4.59!NFATC2;;chr11:65686776..65686787,+!p9@DRAP1!0.59!3.57!DRAP1;;chr11:65667884..65667895,-!p2@FOSL1!0.58!13.00!FOSL1;;chr10:119302232..119302265,+!p1@EMX2!0.58!2.80!EMX2;;chr12:54378923..54378966,+!p1@HOXC10!0.58!2.80!HOXC10;;chr12:54394059..54394088,+!p3@HOXC9!0.58!2.80!HOXC9;;chr2:105470599..105470610,+!p@chr2:105470599..105470610,+!0.58!2.80!POU3F3;;chr3:141043050..141043063,+!p22@ZBTB38!0.58!2.80!ZBTB38;;chr5:3595977..3595999,+!p1@IRX1!0.58!2.80!IRX1;;chr6:34210478..34210481,+!p8@HMGA1!0.58!2.80!HMGA1;;chr7:27190547..27190591,-!p1@HOXA6!0.58!2.80!HOXA6;;chr7:27213893..27213954,-!p1@HOXA10!0.58!2.80!HOXA10;;chr15:67357924..67357952,+!p2@SMAD3!0.57!21.92!SMAD3;;chr1:8938736..8938756,-!p1@ENO1!0.56!3624.34!ENO1;;chr1:8938766..8938774,-!p2@ENO1!0.56!225.31!ENO1;;chr18:3450161..3450183,+!p1@TGIF1!0.56!111.38!TGIF1;;chr12:2986275..2986363,-!p1@FOXM1!0.56!32.62!FOXM1;;chr15:96869255..96869291,+!p6@NR2F2!0.56!5.35!NR2F2;;chr20:50721803..50721857,-!p2@ZFP64!0.56!4.59!ZFP64;;chr22:21355896..21355920,-!p4@THAP7!0.56!3.06!THAP7;;chr10:104154246..104154347,+!p3@NFKB2!0.55!19.12!NFKB2;;chr17:46621937..46621966,-!p2@HOXB2!0.55!8.16!HOXB2;;chr11:64764435..64764449,-!p1@BATF2!0.55!3.82!BATF2;;chr12:54447599..54447630,+!p3@HOXC4!0.55!3.31!HOXC4;;chr12:54402745..54402788,+!p1@HOXC8!0.55!2.55!HOXC8;;chr16:51185573..51185593,-!p3@SALL1!0.55!2.55!SALL1;;chr17:46691732..46691766,-!p4@HOXB8!0.55!2.55!HOXB8;;chr17:46692603..46692621,-!p6@HOXB8!0.55!2.55!HOXB8;;chr5:3595934..3595957,+!p2@IRX1!0.55!2.55!IRX1;;chr3:141043020..141043049,+!p17@ZBTB38!0.55!2.55!ZBTB38;;chr1:8938709..8938720,-!p3@ENO1!0.54!152.16!ENO1;;chr17:7492684..7492778,-!p2@SOX15!0.53!5.86!SOX15;;chr15:96869114..96869160,+!p11@NR2F2!0.53!3.57!NR2F2;;chr6:44233252..44233296,-!p1@NFKBIE!0.52!29.06!NFKBIE;;chr22:42229210..42229229,+!p3@SREBF2!0.52!6.37!SREBF2;;chr6:1610293..1610310,+!p1@FOXC1!0.52!4.33!FOXC1;;chr17:53342311..53342400,+!p1@HLF!0.52!2.80!HLF;;chr16:52581025..52581072,-!p1@TOX3!0.52!2.29!TOX3;;chr17:46621146..46621180,-!p10@HOXB2!0.52!2.29!HOXB2;;chr6:100912785..100912822,-!p1@SIM1!0.52!2.29!SIM1;;chr6:134210243..134210257,+!p1@TCF21!0.52!2.29!TCF21;;chr9:100615499..100615519,+!p1@FOXE1!0.52!2.29!FOXE1;;chr10:119302645..119302712,+!p3@EMX2!0.52!2.29!EMX2;;chr11:65554563..65554576,+!p2@OVOL1!0.52!2.29!OVOL1;;chr1:10856694..10856715,-!p3@CASZ1!0.52!2.29!CASZ1;;chr2:176987463..176987479,+!p2@HOXD9!0.52!2.29!HOXD9;;chr2:176994919..176994931,+!p2@HOXD8!0.52!2.29!HOXD8;;chr2:177001290..177001315,+!p1@HOXD3!0.52!2.29!HOXD3;;chr2:95963052..95963106,+!p1@KCNIP3!0.52!2.29!KCNIP3;;chr9:117160738..117160782,-!p2@AKNA!0.51!11.47!AKNA;;chr3:12329358..12329393,+!p3@PPARG!0.51!6.63!PPARG;;chr3:24536253..24536328,-!p1@THRB!0.51!4.84!THRB;;chr17:41622765..41622821,-!p2@ETV4!0.51!3.82!ETV4;;chr10:8096772..8096787,+!p2@GATA3!0.51!2.80!GATA3;;chr19:45908292..45908374,-!p1@PPP1R13L!0.50!24.98!PPP1R13L;;chr17:47492252..47492265,-!p2@PHB!0.50!11.21!PHB;;chr19:20188776..20188826,+!p1@ZNF90!0.50!7.14!ZNF90;;chr16:8962544..8962584,-!p2@CARHSP1!0.50!5.86!CARHSP1;;chr16:54320675..54320715,-!p1@IRX3!0.50!5.61!IRX3;;chr6:10412392..10412409,-!p4@TFAP2A!0.50!2.55!TFAP2A;;chr6:34204973..34204990,+!p4@HMGA1!0.49!37.47!HMGA1;;chr22:42229246..42229270,+!p2@SREBF2!0.49!34.92!SREBF2;;chr2:239148671..239148686,-!p1@HES6!0.49!9.69!HES6;;chr1:8926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@@ Line 45: / Line 45: @@
 |is_obsolete=
 |library_id=CNhs11330
-|library_id_phase_based=1:CNhs11330
+|library_id_phase_based=2:CNhs11330
-|name=Renal Proximal Tubular Epithelial Cell, donor1
+|name="Renal Proximal Tubular Epithelial Cell, donor1"
 |namespace=FANTOM5
 |part_of=
 |profile_cagescan=,,,
-|profile_hcage=CNhs11330,LSID768,release014,COMPLETED
+|profile_hcage="CNhs11330,LSID768,release014,COMPLETED"
-|profile_rnaseq=,,,
+|profile_rnaseq=
-|profile_srnaseq=SRhi10014,,,
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@@ Line 72: / Line 72: @@
 |sample_cell_line=
 |sample_cell_lot=N/A
-|sample_cell_type=epithelial cell of kidney, proximal tubule
+|sample_cell_type="epithelial cell of kidney, proximal tubule"
 |sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
 |sample_company=Sciencell/3H

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FF:11515-119H3: Difference between revisions

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Revision as of 18:37, 27 November 2014

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