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{{f5samples
{{f5samples
|DRA_sample_Accession=CAGE@SAMD00005004
|DRA_sample_Accession=CAGE@SAMD00005004
|accession_numbers=CAGE;DRX008767;DRR009639;DRZ001064;DRZ002449
|accession_numbers=CAGE;DRX008767;DRR009639;DRZ001064;DRZ002449;DRZ012414;DRZ013799
|ancestors_in_anatomy_facet=
|ancestors_in_anatomy_facet=
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000473,CL:0000255,CL:0000627,CL:0000682
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0000066,CL:0002371,CL:0000473,CL:0000255,CL:0000627,CL:0000682
Line 96: Line 96:
|top_motifs=ZEB1:2.6863348467;HNF4A_NR2F1,2:2.52998773865;NFKB1_REL_RELA:2.15677212293;SNAI1..3:2.09441164058;FOSL2:2.09246698317;ESRRA:2.03860094931;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.96564828493;NR6A1:1.78904560529;TBX4,5:1.76831738912;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.76379610421;HNF1A:1.72352542438;NFIX:1.67387810048;FOXN1:1.62491329954;NR1H4:1.56869611447;PPARG:1.51724619174;ARID5B:1.47309170227;FOXM1:1.26494319529;STAT5{A,B}:1.23323876032;FOS_FOS{B,L1}_JUN{B,D}:1.19195806093;IRF1,2:1.15883904237;ELK1,4_GABP{A,B1}:1.13069628858;PAX2:1.06723586622;AR:1.06711008653;bHLH_family:1.05298236249;ATF6:1.04602050232;MYOD1:1.04476382573;BACH2:0.938986423012;ATF5_CREB3:0.921852940052;HES1:0.90837977147;STAT1,3:0.897697791502;ADNP_IRX_SIX_ZHX:0.895073514077;ATF4:0.894192177389;LMO2:0.860866933643;STAT2,4,6:0.834564031253;PAX8:0.830020413075;TP53:0.827540805081;PDX1:0.809579504571;FOX{I1,J2}:0.77078755672;DMAP1_NCOR{1,2}_SMARC:0.744056257357;SP1:0.724401241739;NR5A1,2:0.685305457938;YY1:0.681472524471;LHX3,4:0.572860910485;GTF2A1,2:0.478397905171;XCPE1{core}:0.457723633032;TBP:0.440837198946;T:0.429398274496;CREB1:0.408574426035;HLF:0.405404021363;ONECUT1,2:0.385794315256;ZBTB6:0.363744577638;SPI1:0.358999564319;ZNF148:0.306845152427;ELF1,2,4:0.294433041148;VSX1,2:0.291908416662;ETS1,2:0.233858663062;POU2F1..3:0.231966532459;FOXL1:0.189819016911;TLX1..3_NFIC{dimer}:0.140223736954;ALX4:0.128952610371;EBF1:0.0996539539557;IRF7:0.089257946165;FOXA2:0.0694082225088;NFE2:0.0605208853016;ESR1:0.0170583004495;GATA6:0.0142175520479;NFY{A,B,C}:0.00479813419885;NKX6-1,2:-0.0361747825078;RXRA_VDR{dimer}:-0.0406616151526;MYB:-0.0477333011598;PAX6:-0.0660820777632;NFE2L2:-0.0796003733787;FOX{D1,D2}:-0.10022915273;CDX1,2,4:-0.101389723243;JUN:-0.125313754215;TFCP2:-0.143134001693;FOXO1,3,4:-0.14798480354;CRX:-0.178118715025;CUX2:-0.204558457166;POU1F1:-0.22977454009;NANOG:-0.249626848293;HIF1A:-0.250491573033;LEF1_TCF7_TCF7L1,2:-0.319343018562;RUNX1..3:-0.348751437994;GFI1:-0.366802526202;ZNF423:-0.395908195388;E2F1..5:-0.415181658625;SRF:-0.41970962792;ZNF143:-0.434514822653;TFAP4:-0.454728007856;OCT4_SOX2{dimer}:-0.456479703551;HSF1,2:-0.466631846437;MAFB:-0.473718515724;TEAD1:-0.531812270104;POU5F1:-0.556157188958;SREBF1,2:-0.572601636997;RORA:-0.5736358251;HBP1_HMGB_SSRP1_UBTF:-0.584428565662;NKX3-2:-0.624273098348;FOX{F1,F2,J1}:-0.648738632128;MED-1{core}:-0.657188263932;SOX17:-0.659382386282;FOXQ1:-0.662651203663;GFI1B:-0.676901970131;MEF2{A,B,C,D}:-0.687917913344;RFX1:-0.714223425751;EP300:-0.719733199073;HOX{A4,D4}:-0.723659684592;REST:-0.731563347078;TAL1_TCF{3,4,12}:-0.743987657703;NRF1:-0.749226017416;NFE2L1:-0.750179032033;POU6F1:-0.759270607737;TLX2:-0.842341550413;PRRX1,2:-0.846839198648;PAX5:-0.861564054512;NANOG{mouse}:-0.869911574033;AHR_ARNT_ARNT2:-0.878096089582;NFIL3:-0.918366004039;TFAP2B:-0.925278676968;TFAP2{A,C}:-0.946801581107;RFX2..5_RFXANK_RFXAP:-0.948242850788;SOX{8,9,10}:-0.967063316921;SPIB:-0.968266080707;ZFP161:-0.969678465257;HIC1:-0.979200189485;PAX1,9:-0.99047785731;CEBPA,B_DDIT3:-0.993452221101;HMX1:-1.00178634278;MAZ:-1.00727136502;POU3F1..4:-1.00823410962;GZF1:-1.02971914936;RXR{A,B,G}:-1.03064758261;HOX{A5,B5}:-1.03818486821;EGR1..3:-1.07693792047;CDC5L:-1.0903950925;SPZ1:-1.09407181163;SOX2:-1.10708318577;UFEwm:-1.13067594041;MYFfamily:-1.16468202476;PBX1:-1.17655157618;NKX2-3_NKX2-5:-1.17753975916;MTF1:-1.19578206037;NR3C1:-1.22209994289;FOXP3:-1.24402799888;BPTF:-1.24463637043;NHLH1,2:-1.24887056074;AIRE:-1.251390335;ATF2:-1.28446355332;TGIF1:-1.28722660447;GTF2I:-1.30991825906;HAND1,2:-1.31689544547;SMAD1..7,9:-1.31907249425;PITX1..3:-1.32111535534;DBP:-1.32180130034;NKX2-1,4:-1.3227270207;EVI1:-1.3396214147;BREu{core}:-1.34171992262;ZBTB16:-1.34220135273;GCM1,2:-1.37195560335;MTE{core}:-1.39833174264;NKX2-2,8:-1.413660994;MYBL2:-1.42646063722;TOPORS:-1.4354321779;RBPJ:-1.44511166048;SOX5:-1.45432008808;KLF4:-1.46601217384;ZNF384:-1.48404153085;HOXA9_MEIS1:-1.50276979574;ZNF238:-1.52359505133;PATZ1:-1.54126298287;TFDP1:-1.55675587225;MZF1:-1.60852194889;PRDM1:-1.75207823002;RREB1:-1.76865261167;GLI1..3:-1.80578530994;ZIC1..3:-1.83364749674;ALX1:-1.8759950111;GATA4:-1.91080652894;NFATC1..3:-1.91644227014;PAX4:-1.93531104423;HMGA1,2:-1.97028040267;IKZF1:-1.99965231551;FOXD3:-2.05470497939;FOXP1:-2.12142480437;EN1,2:-2.14254822203;NKX3-1:-2.22253773716;TEF:-2.26365819271;IKZF2:-2.26866314872
|top_motifs=ZEB1:2.6863348467;HNF4A_NR2F1,2:2.52998773865;NFKB1_REL_RELA:2.15677212293;SNAI1..3:2.09441164058;FOSL2:2.09246698317;ESRRA:2.03860094931;RXR{A,B,G}_{NR1H2,PPAR}dimers:1.96564828493;NR6A1:1.78904560529;TBX4,5:1.76831738912;ARNT_ARNT2_BHLHB2_MAX_MYC_USF1:1.76379610421;HNF1A:1.72352542438;NFIX:1.67387810048;FOXN1:1.62491329954;NR1H4:1.56869611447;PPARG:1.51724619174;ARID5B:1.47309170227;FOXM1:1.26494319529;STAT5{A,B}:1.23323876032;FOS_FOS{B,L1}_JUN{B,D}:1.19195806093;IRF1,2:1.15883904237;ELK1,4_GABP{A,B1}:1.13069628858;PAX2:1.06723586622;AR:1.06711008653;bHLH_family:1.05298236249;ATF6:1.04602050232;MYOD1:1.04476382573;BACH2:0.938986423012;ATF5_CREB3:0.921852940052;HES1:0.90837977147;STAT1,3:0.897697791502;ADNP_IRX_SIX_ZHX:0.895073514077;ATF4:0.894192177389;LMO2:0.860866933643;STAT2,4,6:0.834564031253;PAX8:0.830020413075;TP53:0.827540805081;PDX1:0.809579504571;FOX{I1,J2}:0.77078755672;DMAP1_NCOR{1,2}_SMARC:0.744056257357;SP1:0.724401241739;NR5A1,2:0.685305457938;YY1:0.681472524471;LHX3,4:0.572860910485;GTF2A1,2:0.478397905171;XCPE1{core}:0.457723633032;TBP:0.440837198946;T:0.429398274496;CREB1:0.408574426035;HLF:0.405404021363;ONECUT1,2:0.385794315256;ZBTB6:0.363744577638;SPI1:0.358999564319;ZNF148:0.306845152427;ELF1,2,4:0.294433041148;VSX1,2:0.291908416662;ETS1,2:0.233858663062;POU2F1..3:0.231966532459;FOXL1:0.189819016911;TLX1..3_NFIC{dimer}:0.140223736954;ALX4:0.128952610371;EBF1:0.0996539539557;IRF7:0.089257946165;FOXA2:0.0694082225088;NFE2:0.0605208853016;ESR1:0.0170583004495;GATA6:0.0142175520479;NFY{A,B,C}:0.00479813419885;NKX6-1,2:-0.0361747825078;RXRA_VDR{dimer}:-0.0406616151526;MYB:-0.0477333011598;PAX6:-0.0660820777632;NFE2L2:-0.0796003733787;FOX{D1,D2}:-0.10022915273;CDX1,2,4:-0.101389723243;JUN:-0.125313754215;TFCP2:-0.143134001693;FOXO1,3,4:-0.14798480354;CRX:-0.178118715025;CUX2:-0.204558457166;POU1F1:-0.22977454009;NANOG:-0.249626848293;HIF1A:-0.250491573033;LEF1_TCF7_TCF7L1,2:-0.319343018562;RUNX1..3:-0.348751437994;GFI1:-0.366802526202;ZNF423:-0.395908195388;E2F1..5:-0.415181658625;SRF:-0.41970962792;ZNF143:-0.434514822653;TFAP4:-0.454728007856;OCT4_SOX2{dimer}:-0.456479703551;HSF1,2:-0.466631846437;MAFB:-0.473718515724;TEAD1:-0.531812270104;POU5F1:-0.556157188958;SREBF1,2:-0.572601636997;RORA:-0.5736358251;HBP1_HMGB_SSRP1_UBTF:-0.584428565662;NKX3-2:-0.624273098348;FOX{F1,F2,J1}:-0.648738632128;MED-1{core}:-0.657188263932;SOX17:-0.659382386282;FOXQ1:-0.662651203663;GFI1B:-0.676901970131;MEF2{A,B,C,D}:-0.687917913344;RFX1:-0.714223425751;EP300:-0.719733199073;HOX{A4,D4}:-0.723659684592;REST:-0.731563347078;TAL1_TCF{3,4,12}:-0.743987657703;NRF1:-0.749226017416;NFE2L1:-0.750179032033;POU6F1:-0.759270607737;TLX2:-0.842341550413;PRRX1,2:-0.846839198648;PAX5:-0.861564054512;NANOG{mouse}:-0.869911574033;AHR_ARNT_ARNT2:-0.878096089582;NFIL3:-0.918366004039;TFAP2B:-0.925278676968;TFAP2{A,C}:-0.946801581107;RFX2..5_RFXANK_RFXAP:-0.948242850788;SOX{8,9,10}:-0.967063316921;SPIB:-0.968266080707;ZFP161:-0.969678465257;HIC1:-0.979200189485;PAX1,9:-0.99047785731;CEBPA,B_DDIT3:-0.993452221101;HMX1:-1.00178634278;MAZ:-1.00727136502;POU3F1..4:-1.00823410962;GZF1:-1.02971914936;RXR{A,B,G}:-1.03064758261;HOX{A5,B5}:-1.03818486821;EGR1..3:-1.07693792047;CDC5L:-1.0903950925;SPZ1:-1.09407181163;SOX2:-1.10708318577;UFEwm:-1.13067594041;MYFfamily:-1.16468202476;PBX1:-1.17655157618;NKX2-3_NKX2-5:-1.17753975916;MTF1:-1.19578206037;NR3C1:-1.22209994289;FOXP3:-1.24402799888;BPTF:-1.24463637043;NHLH1,2:-1.24887056074;AIRE:-1.251390335;ATF2:-1.28446355332;TGIF1:-1.28722660447;GTF2I:-1.30991825906;HAND1,2:-1.31689544547;SMAD1..7,9:-1.31907249425;PITX1..3:-1.32111535534;DBP:-1.32180130034;NKX2-1,4:-1.3227270207;EVI1:-1.3396214147;BREu{core}:-1.34171992262;ZBTB16:-1.34220135273;GCM1,2:-1.37195560335;MTE{core}:-1.39833174264;NKX2-2,8:-1.413660994;MYBL2:-1.42646063722;TOPORS:-1.4354321779;RBPJ:-1.44511166048;SOX5:-1.45432008808;KLF4:-1.46601217384;ZNF384:-1.48404153085;HOXA9_MEIS1:-1.50276979574;ZNF238:-1.52359505133;PATZ1:-1.54126298287;TFDP1:-1.55675587225;MZF1:-1.60852194889;PRDM1:-1.75207823002;RREB1:-1.76865261167;GLI1..3:-1.80578530994;ZIC1..3:-1.83364749674;ALX1:-1.8759950111;GATA4:-1.91080652894;NFATC1..3:-1.91644227014;PAX4:-1.93531104423;HMGA1,2:-1.97028040267;IKZF1:-1.99965231551;FOXD3:-2.05470497939;FOXP1:-2.12142480437;EN1,2:-2.14254822203;NKX3-1:-2.22253773716;TEF:-2.26365819271;IKZF2:-2.26866314872
|xref=
|xref=
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_mouse;search_select_hide=table111:11847-124I2;search_select_hide=table117:11847-124I2
}}
}}

Latest revision as of 18:23, 4 June 2020


Name:GP2+ M cell, pool3
Species:Mouse (Mus musculus)
Library ID:CNhs13240
Sample type:primary cells
Genomic View: UCSC
CAGEd-oPOSSUM:link
ZENBU report :link
Additional information
Sample information
strainBalb/c
tissueileum
dev stageadult
sexmale
ageNA
cell typeM cell
cell lineNA
companyNA
collaborationShinji Fukuda (RCAI)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberM cell_c
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0

CAGE Accession numbers
MethodSample accession id
CAGE  SAMD00005004
Library accession numbers

Library idMethodExp. accession idRun accession id
CNhs13240 CAGE DRX008767 DRR009639
Accession ID Mm9

Library idBAMCTSS
CNhs13240 DRZ001064 DRZ002449
Accession ID Mm10

Library idBAMCTSS
CNhs13240 DRZ012414 DRZ013799
Download raw sequence, BAM & CTSS
Mm9
FastaBAMCTSS
downloaddownloaddonwload
Mm10
BAMCTSS
downloaddonwload


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. <br>Analyst:NA <br><br>link to dataset.<br>data

CNhs13240

00
10
100
1000
1000-0.0355
1001-0.0749
1002-0.116
1003-0.123
10040
10051.131
1006-0.364
10070.0188
10081.884
1009-0.157
101-0.137
10100
1011-0.337
10120
10130.368
1014-0.0874
1015-0.258
1016-0.465
10170
10180.648
10190
1020
10200
10210
1022-0.0931
10230
1024-0.291
1025-0.00155
10260
1027-0.048
10280
1029-0.0912
103-0.0887
10300
1031-0.961
10320.872
10330.00952
10340
10350
1036-0.186
10370
1038-0.0435
10390.0748
1040
1040-0.79
10410



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



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: CNhs13240

Jaspar motifP-value
MA0002.20.034
MA0003.10.338
MA0004.10.657
MA0006.10.105
MA0007.10.322
MA0009.10.132
MA0014.10.0594
MA0017.12.5709e-27
MA0018.20.266
MA0019.10.067
MA0024.10.0334
MA0025.10.739
MA0027.10.908
MA0028.10.00967
MA0029.10.862
MA0030.10.746
MA0031.10.488
MA0035.21.35321e-5
MA0038.10.685
MA0039.25.58813e-6
MA0040.10.0843
MA0041.10.231
MA0042.10.278
MA0043.10.552
MA0046.11.85992e-55
MA0047.20.0153
MA0048.10.211
MA0050.12.88541e-4
MA0051.12.3227e-5
MA0052.10.24
MA0055.10.13
MA0057.10.0538
MA0058.10.71
MA0059.10.874
MA0060.10.419
MA0061.10.00104
MA0062.25.08219e-6
MA0065.26.99639e-15
MA0066.10.132
MA0067.10.812
MA0068.10.101
MA0069.10.779
MA0070.10.158
MA0071.10.068
MA0072.10.83
MA0073.10.972
MA0074.10.297
MA0076.10.041
MA0077.10.365
MA0078.10.701
MA0079.20.447
MA0080.27.24917e-6
MA0081.10.739
MA0083.10.227
MA0084.10.185
MA0087.10.263
MA0088.10.207
MA0090.10.623
MA0091.10.298
MA0092.10.607
MA0093.10.702
MA0099.21.06378e-11
MA0100.10.903
MA0101.12.32481e-6
MA0102.20.602
MA0103.13.14102e-7
MA0104.20.441
MA0105.10.0585
MA0106.10.313
MA0107.11.47958e-6
MA0108.26.72333e-4
MA0111.10.454
MA0112.20.00298
MA0113.10.738
MA0114.17.61666e-32
MA0115.11.20966e-16
MA0116.10.245
MA0117.10.351
MA0119.10.122
MA0122.10.877
MA0124.10.611
MA0125.10.998
MA0131.10.93
MA0135.10.176
MA0136.13.32226e-11
MA0137.20.00282
MA0138.20.981
MA0139.10.151
MA0140.10.131
MA0141.11.93406e-6
MA0142.10.0451
MA0143.10.121
MA0144.17.38099e-4
MA0145.10.0132
MA0146.10.101
MA0147.10.558
MA0148.10.016
MA0149.10.0282
MA0150.10.0119
MA0152.10.165
MA0153.11.27712e-45
MA0154.10.0503
MA0155.10.85
MA0156.13.39389e-6
MA0157.10.738
MA0159.15.20485e-4
MA0160.14.31782e-5
MA0162.10.64
MA0163.10.275
MA0164.10.834
MA0258.10.0558
MA0259.10.841



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: CNhs13240

Novel motifP-value
10.172
100.205
1000.895
1010.69
1020.85
1030.465
1040.969
1050.193
1060.0197
1070.142
1080.651
1090.0345
110.143
1100.404
1110.155
1120.0284
1130.164
1140.213
1150.892
1160.0915
1170.027
1180.589
1190.143
120.654
1200.442
1210.247
1220.995
1230.0974
1240.108
1250.592
1260.0665
1270.235
1280.22
1290.19
133.16139e-5
1300.871
1310.897
1320.743
1330.493
1340.958
1350.103
1360.00744
1370.81
1380.265
1390.188
140.751
1400.882
1410.153
1420.988
1430.146
1440.166
1450.148
1460.24
1470.792
1480.839
1490.857
150.117
1500.421
1510.985
1520.0268
1530.85
1540.742
1550.366
1560.0715
1570.409
1580.661
1590.714
1600.872
1610.805
1620.551
1630.061
1640.0963
1650.153
1660.647
1670.771
1680.938
1690.0262
170.0401
180.85
190.297
20.846
200.308
210.981
220.276
230.539
240.456
250.455
260.0126
270.995
280.34
290.0798
30.196
300.353
310.923
320.257
330.195
340.881
350.968
360.581
370.0254
380.429
390.386
40.202
400.214
410.134
420.75
430.311
440.152
450.365
460.408
470.417
480.224
490.445
50.738
500.387
510.677
520.164
530.458
540.43
550.503
560.5
570.844
580.274
590.246
60.65
600.031
610.303
620.227
630.0951
640.722
650.296
660.826
670.479
680.0769
690.957
70.0651
700.0142
710.169
720.256
730.0226
740.663
750.0171
760.733
770.0558
780.0195
790.803
80.334
800.913
810.973
820.16
830.533
840.123
850.149
860.151
870.00562
880.259
890.281
90.979
900.311
910.925
920.562
930.23
940.745
950.00213
960.979
970.813
980.509
990.42



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: CNhs13240


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)
0000473 (defensive cell)
0000255 (eukaryotic cell)
0000627 (transporting cell)
0000682 (M cell of gut)

FF: FANTOM5
0000102 (sample by type)
0000002 (in vivo cell sample)
0000101 (sample by species)
0000103 (mouse sample)
0000001 (sample)
0011159 (mouse GP2-positive M 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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