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{{f5samples
{{f5samples
|id=FF:12127-128D3
|ancestors_in_anatomy_facet=
|name=stem cell (cKit+ Sca1- lineage-) KSL, biol_rep3
|sample_id=12127
|rna_tube_id=128D3
|rna_box=128
|rna_position=D3
|sample_cell_lot=
|sample_cell_catalog=
|sample_company=
|rna_lot_number=rep3
|rna_catalog_number=
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/8J
|sample_dev_stage=
|sample_tissue=bone marrow
|sample_donor(cell lot)=21 pool
|sample_sex=male
|sample_age=9-10weeks
|sample_ethnicity=
|rna_rin=
|rna_od260/230=1.240111182
|rna_od260/280=1.676300578
|sample_cell_type=stem cell (cKit+ Sca1- lineage-)
|sample_cell_line=
|sample_collaboration=Kitamura/Nakahara
|sample_experimental_condition=
|sample_disease=
|rna_sample_type=total RNA
|rna_extraction_protocol=
|rna_weight_ug=1.02124
|rna_concentration=0.02321
|sample_note=
|profile_hcage=CNhs12536,LSID920,release012,COMPLETED
|profile_cagescan=,,,
|profile_srnaseq=,,,
|profile_rnaseq=,,,
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000012,CL:0000034,CL:0000144
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000012,CL:0000034,CL:0000144
|ancestors_in_anatomy_facet=
|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=ATF4:3.21825584306;CREB1:3.17266667237;NFKB1_REL_RELA:3.1670006629;NFE2:2.84867132623;ATF5_CREB3:2.66928321769;RUNX1..3:2.65626542057;FOS_FOS{B,L1}_JUN{B,D}:2.42194404835;SPI1:2.35575482935;BACH2:2.35016038725;ETS1,2:2.20649477535;ELF1,2,4:2.20088510608;PAX8:2.19028595043;DMAP1_NCOR{1,2}_SMARC:2.18326571866;SPIB:2.16106785997;BPTF:2.10447400534;bHLH_family:1.97957611771;POU2F1..3:1.88078321102;PAX2:1.76138128449;FOXP3:1.56108613151;FOX{I1,J2}:1.51344468775;FOX{D1,D2}:1.3540285215;E2F1..5:1.34947283467;SPZ1:1.31040712959;IRF1,2:1.30312547687;NFATC1..3:1.23621165192;MYB:1.15408004231;PPARG:1.14983036901;FOSL2:1.10816210419;NFE2L1:1.09680209776;ALX4:1.08328929156;YY1:1.08255577658;CEBPA,B_DDIT3:1.07554634604;TBX4,5:1.02416831796;ELK1,4_GABP{A,B1}:1.0235098057;ZNF384:0.80476763471;ATF6:0.705187166348;IRF7:0.698628490668;JUN:0.690491082095;NANOG{mouse}:0.605909883727;STAT2,4,6:0.543950475123;PBX1:0.511811020451;TFDP1:0.511139869055;AIRE:0.504996832952;NKX6-1,2:0.464442679325;HMX1:0.462255516894;POU5F1:0.452473925256;HLF:0.387602136823;ATF2:0.351090634535;ALX1:0.337960570096;ZBTB16:0.316899964079;SREBF1,2:0.306313526002;NFIL3:0.305327093793;NANOG:0.302293646732;FOXN1:0.290855381597;SOX2:0.287131632007;FOXD3:0.217278108411;NFY{A,B,C}:0.21159213069;TP53:0.197884219864;EGR1..3:0.14922806395;HIF1A:0.134327476537;IKZF2:0.111177749568;AHR_ARNT_ARNT2:0.10067227464;TLX2:0.0776851882253;FOXQ1:0.0287812643132;TEF:0.0257875820095;HBP1_HMGB_SSRP1_UBTF:0.0200122793827;SOX17:-0.000226334738016;STAT1,3:-0.0221361509863;NR6A1:-0.0283184999584;PDX1:-0.0357439615669;RFX2..5_RFXANK_RFXAP:-0.0702030997535;GATA6:-0.0958815557005;TBP:-0.102618675036;ZNF148:-0.11994060792;STAT5{A,B}:-0.12871028268;NFE2L2:-0.13135841139;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.147292750329;PITX1..3:-0.147617670415;CRX:-0.173020880643;SP1:-0.173698675052;FOXL1:-0.180549085312;RXR{A,B,G}:-0.183096954707;MEF2{A,B,C,D}:-0.239140936819;NKX2-2,8:-0.251114697757;AR:-0.255537017654;FOXO1,3,4:-0.271916863557;MTF1:-0.297183083241;TFCP2:-0.324811329835;PAX5:-0.364321832483;NRF1:-0.375033106119;ZIC1..3:-0.38280753837;RORA:-0.397896088142;CDC5L:-0.401027302416;HSF1,2:-0.404017281884;SRF:-0.412532394645;FOX{F1,F2,J1}:-0.422137902445;RFX1:-0.422249487782;ONECUT1,2:-0.439984334467;FOXP1:-0.449742068477;ESR1:-0.460408137346;CDX1,2,4:-0.463955686196;CUX2:-0.481295262235;ARID5B:-0.485917132986;BREu{core}:-0.500124612627;MTE{core}:-0.508008452476;PRDM1:-0.515636642768;GATA4:-0.527250179672;TFAP2B:-0.551906452798;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.553742011165;RXRA_VDR{dimer}:-0.559392711969;MAFB:-0.563408857303;PAX1,9:-0.565352933242;ESRRA:-0.570722756104;MED-1{core}:-0.584137326381;MYOD1:-0.586145460277;ZNF143:-0.589360481717;NKX2-3_NKX2-5:-0.603422906794;NR1H4:-0.608150972782;DBP:-0.631820038399;PAX4:-0.637966256219;ZFP161:-0.657624396754;NR5A1,2:-0.675915770139;TFAP2{A,C}:-0.683236543251;EVI1:-0.697604032424;HNF4A_NR2F1,2:-0.719503607606;PAX6:-0.720278078845;HES1:-0.727621440003;HNF1A:-0.73187348813;MZF1:-0.773625513679;HOX{A4,D4}:-0.775570631463;ZBTB6:-0.797793045348;NHLH1,2:-0.803909821594;MYFfamily:-0.806761643471;LMO2:-0.812910366089;NFIX:-0.834305544014;REST:-0.837500480177;XCPE1{core}:-0.857126902064;EBF1:-0.859627004167;PRRX1,2:-0.867502535439;ZNF238:-0.883758225456;OCT4_SOX2{dimer}:-0.88485651954;ZEB1:-0.885011413113;EN1,2:-0.916452485606;GFI1:-0.921322354961;SNAI1..3:-0.927381182148;EP300:-0.933718098159;RREB1:-0.96302545801;TGIF1:-0.968233380338;SOX5:-0.993316931812;FOXA2:-1.00270320214;SOX{8,9,10}:-1.02689459716;HIC1:-1.07581323181;LEF1_TCF7_TCF7L1,2:-1.08522267383;NR3C1:-1.08830548112;SMAD1..7,9:-1.10229766009;LHX3,4:-1.1056397418;HAND1,2:-1.11264908648;POU1F1:-1.12462127151;POU3F1..4:-1.12557501337;MAZ:-1.15053211524;MYBL2:-1.1860445695;NKX2-1,4:-1.20750519256;GTF2A1,2:-1.20797471338;RBPJ:-1.22535155286;GLI1..3:-1.22646312525;T:-1.22926147422;GTF2I:-1.34284579331;HOX{A5,B5}:-1.35692154169;VSX1,2:-1.3632213163;POU6F1:-1.37099338964;UFEwm:-1.38559121723;PATZ1:-1.4086079749;GZF1:-1.42267985015;TEAD1:-1.46638272614;TLX1..3_NFIC{dimer}:-1.48366014278;ZNF423:-1.48914701713;FOXM1:-1.51881249485;GCM1,2:-1.51989165291;TFAP4:-1.57340533378;TOPORS:-1.6174462329;GFI1B:-1.65059499666;ADNP_IRX_SIX_ZHX:-1.65758687916;KLF4:-1.66418263213;NKX3-1:-1.70886535915;HOXA9_MEIS1:-1.73678381333;TAL1_TCF{3,4,12}:-2.00216071928;HMGA1,2:-2.09779540001;IKZF1:-2.16911058439;NKX3-2:-2.3969849572
|comment=
|created_by=
|creation_date=
|def=
|has_quality=
|has_quality=
|id=FF:12127-128D3
|is_a=EFO:0002091;;FF:0000002;;FF:0000021;;FF:0000103
|is_a=EFO:0002091;;FF:0000002;;FF:0000021;;FF:0000103
|name=stem cell (cKit+ Sca1- lineage-) KSL, biol_rep3
|namespace=FANTOM5
|namespace=FANTOM5
|part_of=
|part_of=
|profile_cagescan=,,,
|profile_hcage=CNhs12536,LSID920,release012,COMPLETED
|profile_rnaseq=,,,
|profile_srnaseq=,,,
|rna_box=128
|rna_catalog_number=
|rna_concentration=0.02321
|rna_extraction_protocol=
|rna_lot_number=rep3
|rna_od260/230=1.240111182
|rna_od260/280=1.676300578
|rna_position=D3
|rna_rin=
|rna_sample_type=total RNA
|rna_tube_id=128D3
|rna_weight_ug=1.02124
|sample_age=9-10weeks
|sample_cell_catalog=
|sample_cell_line=
|sample_cell_lot=
|sample_cell_type=stem cell (cKit+ Sca1- lineage-)
|sample_collaboration=Kitamura/Nakahara
|sample_company=
|sample_description=
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=21 pool
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=12127
|sample_note=
|sample_sex=male
|sample_species=Mouse (Mus musculus)
|sample_strain=C57BL/8J
|sample_tissue=bone marrow
|top_motifs=ATF4:3.21825584306;CREB1:3.17266667237;NFKB1_REL_RELA:3.1670006629;NFE2:2.84867132623;ATF5_CREB3:2.66928321769;RUNX1..3:2.65626542057;FOS_FOS{B,L1}_JUN{B,D}:2.42194404835;SPI1:2.35575482935;BACH2:2.35016038725;ETS1,2:2.20649477535;ELF1,2,4:2.20088510608;PAX8:2.19028595043;DMAP1_NCOR{1,2}_SMARC:2.18326571866;SPIB:2.16106785997;BPTF:2.10447400534;bHLH_family:1.97957611771;POU2F1..3:1.88078321102;PAX2:1.76138128449;FOXP3:1.56108613151;FOX{I1,J2}:1.51344468775;FOX{D1,D2}:1.3540285215;E2F1..5:1.34947283467;SPZ1:1.31040712959;IRF1,2:1.30312547687;NFATC1..3:1.23621165192;MYB:1.15408004231;PPARG:1.14983036901;FOSL2:1.10816210419;NFE2L1:1.09680209776;ALX4:1.08328929156;YY1:1.08255577658;CEBPA,B_DDIT3:1.07554634604;TBX4,5:1.02416831796;ELK1,4_GABP{A,B1}:1.0235098057;ZNF384:0.80476763471;ATF6:0.705187166348;IRF7:0.698628490668;JUN:0.690491082095;NANOG{mouse}:0.605909883727;STAT2,4,6:0.543950475123;PBX1:0.511811020451;TFDP1:0.511139869055;AIRE:0.504996832952;NKX6-1,2:0.464442679325;HMX1:0.462255516894;POU5F1:0.452473925256;HLF:0.387602136823;ATF2:0.351090634535;ALX1:0.337960570096;ZBTB16:0.316899964079;SREBF1,2:0.306313526002;NFIL3:0.305327093793;NANOG:0.302293646732;FOXN1:0.290855381597;SOX2:0.287131632007;FOXD3:0.217278108411;NFY{A,B,C}:0.21159213069;TP53:0.197884219864;EGR1..3:0.14922806395;HIF1A:0.134327476537;IKZF2:0.111177749568;AHR_ARNT_ARNT2:0.10067227464;TLX2:0.0776851882253;FOXQ1:0.0287812643132;TEF:0.0257875820095;HBP1_HMGB_SSRP1_UBTF:0.0200122793827;SOX17:-0.000226334738016;STAT1,3:-0.0221361509863;NR6A1:-0.0283184999584;PDX1:-0.0357439615669;RFX2..5_RFXANK_RFXAP:-0.0702030997535;GATA6:-0.0958815557005;TBP:-0.102618675036;ZNF148:-0.11994060792;STAT5{A,B}:-0.12871028268;NFE2L2:-0.13135841139;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:-0.147292750329;PITX1..3:-0.147617670415;CRX:-0.173020880643;SP1:-0.173698675052;FOXL1:-0.180549085312;RXR{A,B,G}:-0.183096954707;MEF2{A,B,C,D}:-0.239140936819;NKX2-2,8:-0.251114697757;AR:-0.255537017654;FOXO1,3,4:-0.271916863557;MTF1:-0.297183083241;TFCP2:-0.324811329835;PAX5:-0.364321832483;NRF1:-0.375033106119;ZIC1..3:-0.38280753837;RORA:-0.397896088142;CDC5L:-0.401027302416;HSF1,2:-0.404017281884;SRF:-0.412532394645;FOX{F1,F2,J1}:-0.422137902445;RFX1:-0.422249487782;ONECUT1,2:-0.439984334467;FOXP1:-0.449742068477;ESR1:-0.460408137346;CDX1,2,4:-0.463955686196;CUX2:-0.481295262235;ARID5B:-0.485917132986;BREu{core}:-0.500124612627;MTE{core}:-0.508008452476;PRDM1:-0.515636642768;GATA4:-0.527250179672;TFAP2B:-0.551906452798;RXR{A,B,G}_{NR1H2,PPAR}dimers:-0.553742011165;RXRA_VDR{dimer}:-0.559392711969;MAFB:-0.563408857303;PAX1,9:-0.565352933242;ESRRA:-0.570722756104;MED-1{core}:-0.584137326381;MYOD1:-0.586145460277;ZNF143:-0.589360481717;NKX2-3_NKX2-5:-0.603422906794;NR1H4:-0.608150972782;DBP:-0.631820038399;PAX4:-0.637966256219;ZFP161:-0.657624396754;NR5A1,2:-0.675915770139;TFAP2{A,C}:-0.683236543251;EVI1:-0.697604032424;HNF4A_NR2F1,2:-0.719503607606;PAX6:-0.720278078845;HES1:-0.727621440003;HNF1A:-0.73187348813;MZF1:-0.773625513679;HOX{A4,D4}:-0.775570631463;ZBTB6:-0.797793045348;NHLH1,2:-0.803909821594;MYFfamily:-0.806761643471;LMO2:-0.812910366089;NFIX:-0.834305544014;REST:-0.837500480177;XCPE1{core}:-0.857126902064;EBF1:-0.859627004167;PRRX1,2:-0.867502535439;ZNF238:-0.883758225456;OCT4_SOX2{dimer}:-0.88485651954;ZEB1:-0.885011413113;EN1,2:-0.916452485606;GFI1:-0.921322354961;SNAI1..3:-0.927381182148;EP300:-0.933718098159;RREB1:-0.96302545801;TGIF1:-0.968233380338;SOX5:-0.993316931812;FOXA2:-1.00270320214;SOX{8,9,10}:-1.02689459716;HIC1:-1.07581323181;LEF1_TCF7_TCF7L1,2:-1.08522267383;NR3C1:-1.08830548112;SMAD1..7,9:-1.10229766009;LHX3,4:-1.1056397418;HAND1,2:-1.11264908648;POU1F1:-1.12462127151;POU3F1..4:-1.12557501337;MAZ:-1.15053211524;MYBL2:-1.1860445695;NKX2-1,4:-1.20750519256;GTF2A1,2:-1.20797471338;RBPJ:-1.22535155286;GLI1..3:-1.22646312525;T:-1.22926147422;GTF2I:-1.34284579331;HOX{A5,B5}:-1.35692154169;VSX1,2:-1.3632213163;POU6F1:-1.37099338964;UFEwm:-1.38559121723;PATZ1:-1.4086079749;GZF1:-1.42267985015;TEAD1:-1.46638272614;TLX1..3_NFIC{dimer}:-1.48366014278;ZNF423:-1.48914701713;FOXM1:-1.51881249485;GCM1,2:-1.51989165291;TFAP4:-1.57340533378;TOPORS:-1.6174462329;GFI1B:-1.65059499666;ADNP_IRX_SIX_ZHX:-1.65758687916;KLF4:-1.66418263213;NKX3-1:-1.70886535915;HOXA9_MEIS1:-1.73678381333;TAL1_TCF{3,4,12}:-2.00216071928;HMGA1,2:-2.09779540001;IKZF1:-2.16911058439;NKX3-2:-2.3969849572
}}
}}

Revision as of 15:06, 21 March 2012


Name:stem cell (cKit+ Sca1- lineage-) KSL, biol_rep3
Species:Mouse (Mus musculus)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainC57BL/8J
tissuebone marrow
dev stageNA
sexmale
age9-10weeks
cell typestem cell (cKit+ Sca1- lineage-)
cell lineNA
companyNA
collaborationKitamura/Nakahara
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberrep3
catalog numberNA
sample typetotal RNA
extraction protocol (Details)NA
Download raw sequence, BAM & CTSS
CollapseMm9
BAMCTSS
[{{{mm9bam}}} download][{{{mm9ctss}}} donwload]
CollapseMm10
BAMCTSS
[{{{mm10bam}}} download][{{{mm10ctss}}} 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>data

CNhs12536



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: CNhs12536



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: CNhs12536



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: CNhs12536


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)

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