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{{f5samples
{{f5samples
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000966,UBERON:0000970,UBERON:0000019,UBERON:0000483,UBERON:0000033,UBERON:0000479,UBERON:0002346,UBERON:0000064,UBERON:0000073,UBERON:0000047,UBERON:0004121,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0000480,UBERON:0000923,UBERON:0002050,UBERON:0004923,UBERON:0005423,UBERON:0001444,UBERON:0000481,UBERON:0000467,UBERON:0001062,UBERON:0000119,UBERON:0005291,UBERON:0005388,UBERON:0000020,UBERON:0007625,UBERON:0001781,UBERON:0001032,UBERON:0005085,UBERON:0001048,UBERON:0006598,UBERON:0002532,UBERON:0001782,UBERON:0001016,UBERON:0004088,UBERON:0000153,UBERON:0007811,UBERON:0000924,UBERON:0002104,UBERON:0001802,UBERON:0005743,UBERON:0004456,UBERON:0001456,UBERON:0003075,UBERON:0003056,UBERON:0003072,UBERON:0003071,UBERON:0006601,UBERON:0004128,UBERON:0005424,UBERON:0007284
|DRA_sample_Accession=CAGE@SAMD00005253
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000144,CL:0000548,CL:0000012,CL:0000063,CL:0000066,CL:0002371,CL:0000325,CL:0000147,CL:0000004,CL:0000255,CL:0000149,CL:0002586
|DRA_sample_Accession_RNASeq=sRNA-Seq@SAMD00005253
|accession_numbers=CAGE;DRX008442;DRR009314;DRZ000739;DRZ002124;DRZ012089;DRZ013474
|accession_numbers_RNASeq=sRNA-Seq;DRX037095;DRR041461;DRZ007103
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000966,UBERON:0000970,UBERON:0000019,UBERON:0000483,UBERON:0000033,UBERON:0000479,UBERON:0004121,UBERON:0000064,UBERON:0010314,UBERON:0000047,UBERON:0000062,UBERON:0000475,UBERON:0000061,UBERON:0000465,UBERON:0000063,UBERON:0004923,UBERON:0001444,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0005388,UBERON:0000020,UBERON:0010371,UBERON:0007625,UBERON:0001781,UBERON:0001032,UBERON:0010317,UBERON:0001782,UBERON:0004088,UBERON:0000153,UBERON:0007811,UBERON:0002104,UBERON:0001802,UBERON:0004456,UBERON:0001456,UBERON:0010230
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000325,CL:0000147,CL:0000255,CL:0000149,CL:0002586
|ancestors_in_disease_facet=
|ancestors_in_disease_facet=
|ancestors_in_ff_facet=FF:0000102,FF:0000210,FF:0000002,FF:0000101,FF:0000001,FF:0000158
|comment=
|comment=
|created_by=
|created_by=
|creation_date=
|creation_date=
|data_phase=2
|datafreeze_phase=2
|def=
|def=
|fonse_cell_line=
|fonse_cell_line=
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|fonse_treatment_closure=
|fonse_treatment_closure=
|has_quality=
|has_quality=
|hg19bam=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Retinal%2520Pigment%2520Epithelial%2520Cells%252c%2520donor2.CNhs12096.11608-120I6.hg19.nobarcode.bam
|hg19ctss=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Retinal%2520Pigment%2520Epithelial%2520Cells%252c%2520donor2.CNhs12096.11608-120I6.hg19.ctss.bed.gz
|hg19fasta=http://fantom.gsc.riken.jp/5/datafiles/latest/basic/human.primary_cell.hCAGE/Retinal%2520Pigment%2520Epithelial%2520Cells%252c%2520donor2.CNhs12096.11608-120I6.hg19.nobarcode.rdna.fa.gz
|hg38bam=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Retinal%2520Pigment%2520Epithelial%2520Cells%252c%2520donor2.CNhs12096.11608-120I6.hg38.nobarcode.bam
|hg38ctss=http://fantom.gsc.riken.jp/5/datafiles/reprocessed/hg38_v2/basic/human.primary_cell.hCAGE/Retinal%2520Pigment%2520Epithelial%2520Cells%252c%2520donor2.CNhs12096.11608-120I6.hg38.nobarcode.ctss.bed.gz
|id=FF:11608-120I6
|id=FF:11608-120I6
|is_a=EFO:0002091;;FF:0000002;;FF:0000158;;FF:0000210
|is_a=EFO:0002091;;FF:0000158
|is_obsolete=
|library_id=CNhs12096
|library_id_phase_based=2:CNhs12096
|microRNAs=
|microRNAs_nn=
|microRNAs_nonnovel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer/#/human#cage;sample;11608
|microRNAs_nonnovel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer/#/human#srna;sample;SRhi10007.GATCAG.11608
|microRNAs_novel_cage=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2017/vis_viewer_novel/#/human#cage;sample;11608
|microRNAs_novel_srna=http://fantom.gsc.riken.jp/5/suppl/De_Rie_et_al_2016/vis_viewer_novel/#/human#srna;sample;SRhi10007.GATCAG.11608
|name=Retinal Pigment Epithelial Cells, donor2
|name=Retinal Pigment Epithelial Cells, donor2
|namespace=FANTOM5
|namespace=FANTOM5
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|profile_cagescan=,,,
|profile_cagescan=,,,
|profile_hcage=CNhs12096,LSID839,release011,COMPLETED
|profile_hcage=CNhs12096,LSID839,release011,COMPLETED
|profile_rnaseq=,,,
|profile_rnaseq=
|profile_srnaseq=SRhi10007,,,
|profile_srnaseq=SRhi10007,,,
|rna_box=120
|rna_box=120
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|rna_tube_id=120I6
|rna_tube_id=120I6
|rna_weight_ug=10
|rna_weight_ug=10
|rnaseq_library_id=SRhi10007.GATCAG
|sample_age=
|sample_age=
|sample_category=primary cells
|sample_cell_catalog=N/A
|sample_cell_catalog=N/A
|sample_cell_line=
|sample_cell_line=
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|sample_tissue=eye
|sample_tissue=eye
|top_motifs=
|top_motifs=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_human;search_select_hide=table111:FF:11608-120I6;search_select_hide=table117:FF:11608-120I6
}}
}}

Latest revision as of 18:11, 4 June 2020


Name:Retinal Pigment Epithelial Cells, donor2
Species:Human (Homo sapiens)
Library ID:CNhs12096
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainNA
tissueeye
dev stageNA
sexNA
ageNA
cell typeretinal pigment epithelial cell
cell lineNA
companySciencell/3H
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberSC6545
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-ethanol-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005253
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs12096 CAGE DRX008442 DRR009314
Accession ID Hg19

Library idBAMCTSS
CNhs12096 DRZ000739 DRZ002124
Accession ID Hg38

Library idBAMCTSS
CNhs12096 DRZ012089 DRZ013474
Download raw sequence, BAM & CTSS
Hg19
FastaBAMCTSS
downloaddownloaddonwload
Hg38
BAMCTSS
downloaddonwload

RNA-Seq Accession numbers
MethodSample accession id
sRNA-Seq  SAMD00005253
Library accession numbers

Library idMethodExp. accession idRun accession id
SRhi10007.GATCAG sRNA-Seq DRX037095 DRR041461
Accession ID Hg19

Library idBAMCTSS
SRhi10007.GATCAG DRZ007103





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: CNhs12096This 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: CNhs12096This 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: CNhs12096


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)
0000548 (animal cell)
0000066 (epithelial cell)
0002371 (somatic cell)
0000325 (stuff accumulating cell)
0000147 (pigment cell)
0000255 (eukaryotic cell)
0000149 (visual pigment cell)
0002586 (retinal pigment epithelial cell)

UBERON: Anatomy
0000468 (multi-cellular organism)
0000966 (retina)
0000970 (eye)
0000019 (camera-type eye)
0000483 (epithelium)
0000033 (head)
0000479 (tissue)
0004121 (ectoderm-derived structure)
0000064 (organ part)
0010314 (structure with developmental contribution from neural crest)
0000047 (simple eye)
0000062 (organ)
0000475 (organism subdivision)
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000063 (organ segment)
0004923 (organ component layer)
0001444 (subdivision of head)
0000477 (anatomical cluster)
0000467 (anatomical system)
0001062 (anatomical entity)
0000480 (anatomical group)
0000119 (cell layer)
0005388 (photoreceptor array)
0000020 (sense organ)
0010371 (ecto-epithelium)
0007625 (pigment epithelium of eye)
0001781 (layer of retina)
0001032 (sensory system)
0010317 (germ layer / neural crest derived structure)
0001782 (pigmented layer of retina)
0004088 (ocular region)
0000153 (anterior region of body)
0007811 (craniocervical region)
0002104 (visual system)
0001802 (posterior segment of eyeball)
0004456 (entire sense organ system)
0001456 (face)
0010230 (eyeball of camera-type eye)

FF: FANTOM5
0000102 (sample by type)
0000210 (human sample)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000001 (sample)
0000158 (human retinal pigment epithelial 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
NA

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