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Platform GPL32543 Query DataSets for GPL32543
Status Public on Aug 04, 2022
Title HorvathMammalMethylChip320
Technology type oligonucleotide beads
Distribution custom-commercial
Organisms Macaca mulatta; Homo sapiens; Mus musculus; Rattus
Manufacturer Illumina, Inc.
Manufacture protocol See manufacturer's website
 
 
Submission date Aug 01, 2022
Last update date Aug 04, 2022
Contact name Steve Horvath
E-mail(s) shorvath@altoslabs.com
Organization name University of California, Los Angeles
Department Human Genetics
Lab Horvath
Street address 695 Charles E. Young Drive South, Box 708822
City Los Angeles
State/province CA
ZIP/Postal code 90095-7088
Country USA
 
Samples (431) GSM6427929, GSM6427930, GSM6427931, GSM6427932, GSM6427933, GSM6427934 
Series (8)
GSE210308 Methylation study of rapamycin treatment during development in mice
GSE223943 P30.Dataset
GSE223944 P31.Dataset

Data table header descriptions
ID
SPOT_ID
SYMBOL
GeneRegionID
mm10.Chr
mm10.Coord.probeStart
mm10.Coord.probeEnd
CGstart
CGend
strand
seq
annotation
geneChr
geneStart
geneEnd
geneLength
geneStrand
transcriptId
distanceToTSS
flank_txIds
flank_geneIds
flank_gene_distances
genic
Intergenic
Promoter
fiveUTR
threeUTR
Exon
Intron
downstream
distal_intergenic
main_Categories
ENTREZID
ENSEMBL
conservationInHuman
CGIslandNess
CG
HumanUniversalChromatinState.stackHMM.Vu.Ernst2022
repeatElements
CpG.island
Brown_rat.corCalibration
Human.corCalibration
Mouse.corCalibration
Rhesus_macaque.corCalibration

Data table
ID SPOT_ID SYMBOL GeneRegionID mm10.Chr mm10.Coord.probeStart mm10.Coord.probeEnd CGstart CGend strand seq annotation geneChr geneStart geneEnd geneLength geneStrand transcriptId distanceToTSS flank_txIds flank_geneIds flank_gene_distances genic Intergenic Promoter fiveUTR threeUTR Exon Intron downstream distal_intergenic main_Categories ENTREZID ENSEMBL conservationInHuman CGIslandNess CG HumanUniversalChromatinState.stackHMM.Vu.Ernst2022 repeatElements CpG.island Brown_rat.corCalibration Human.corCalibration Mouse.corCalibration Rhesus_macaque.corCalibration
cg00101675_BC21 cg00101675 Ppp2r5e Ppp2r5e_fiveUTR 12 75515719 75515768 75515719 75515720 + CGTGTCCATGAAGTCAAAAATGACACAGCACTGCTGAAGTTTCTTTAGGA 5' UTR 12 75450881 75596200 145320 2 Ppp2r5e-201 80432 Ppp2r5e-201;Ppp2r5e-205;Ppp2r5e-202;Ppp2r5e-203;Ppp2r5e-204 Ppp2r5e;Ppp2r5e;Ppp2r5e;Ppp2r5e;Ppp2r5e 0;0;0;0;0 TRUE FALSE FALSE TRUE FALSE TRUE TRUE FALSE FALSE fiveUTR 26932 ENSMUSG00000021051 conserved gene but different region + TRUE TxEnh3 NA no 0.998823279 0.668701058 0.997216418 0.976245013
cg00116289_BC21 cg00116289 Zfr Zfr_Exon 15 12170802 12170851 12170850 12170851 - TCAATCCATTTTAGATGTAACCTCGGGTATGGTGAAAGACCCACCGGACG "Exon (Zfr-201/Zfr exon 16 of 20)" 15 12117831 12185683 67853 1 Zfr-201 52971 Zfr-201;Zfr-207;Zfr-208;Zfr-209;Zfr-206 Zfr;Zfr;Zfr;Zfr;Zfr 0;0;0;0;0 TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE Exon 22763 ENSMUSG00000022201 conserved gene and region + TRUE NA NA no 0.996236159 0.996941278 0.999135375
cg00211372_TC21 cg00211372 Rbmx Rbmx_threeUTR X 57387384 57387433 57387384 57387385 + CGTGAGTTACCTGCAGGGTCAATGGTCAGGTAATATGGCAACACTATAAA 3' UTR 20 57383530 57392981 9452 2 Rbmx-205 5548 Rbmx-205;Rbmx-201;Rbmx-203;Rbmx-202;Rbmx-206;Rbmx-204 Rbmx;Rbmx;Rbmx;Rbmx;Rbmx;Rbmx 0;0;0;0;0;5364 TRUE FALSE FALSE FALSE TRUE TRUE TRUE FALSE FALSE threeUTR 19655 ENSMUSG00000031134 mapped to different genes NA TRUE NA NA yes 0.915102602 0.731385329 0.939051862 0.982045502
cg00531009_BC21 cg00531009 NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA no 0.899874283 0.76490978 0.952117493 0.909108226
cg00896209_TC21 cg00896209 Clk2 Clk2_Exon 3 89169680 89169729 89169680 89169681 - CGGGGACTGGCTACAAGAGCGATGTACAAGCCAAATCGTAACAATCCTAT "Exon (Clk2-202/Clk2 exon 4 of 13)" 3 89164795 89176921 12127 1 Clk2-202 4885 Clk2-202;Clk2-210;Clk2-201;Clk2-209;Clk2-207;Clk2-203;Clk2-204;Clk2-206;Clk2-211;Clk2-205 Clk2;Clk2;Clk2;Clk2;Clk2;Clk2;Clk2;Clk2;Clk2;Clk2 0;4863;0;0;0;0;0;0;0;-4226 TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE Exon 12748 ENSMUSG00000068917 conserved gene and region + TRUE TxEx2 NA yes 0.942394722 0.974107544 0.983812899
cg00910419_BC21 cg00910419 Bcl11a Bcl11a_fiveUTR 11 24078020 24078069 24078068 24078069 - CCCATGTTTTGTGTGTCTCTGTCCATCCAGACTCCTGACGTTCAAGTTCG Promoter (<=1kb) 11 24078056 24173194 95139 1 Bcl11a-201 0 A830031A19Rik-201;Bcl11a-201;Bcl11a-203;Bcl11a-205;Bcl11a-202;Bcl11a-204 A830031A19Rik;Bcl11a;Bcl11a;Bcl11a;Bcl11a;Bcl11a 0;0;0;0;0;0 TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE fiveUTR 14025 ENSMUSG00000000861 conserved gene and region + TRUE NA NA no 0.936236452 0.918904191 0.979299402 0.91186119
cg00920372_BC21 cg00920372 Btrc Btrc_Exon 19 45330034 45330083 45330082 45330083 + GGTGACATATCTCTCTTATTGCCCGAATGTAACACACCATCTAATTTACG "Exon (Gm28578-209/Gm28578-209 exon 6 of 7)" 19 45363734 45507736 144003 1 Btrc-204 -33651 NA NA NA TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE Exon 12234 ENSMUSG00000025217 conserved gene and region + TRUE ReprPC5 NA yes 0.984502285 0.999100775 0.999938778
cg01340195_BC21 cg01340195 Tbc1d5 Tbc1d5_Intron 17 51048780 51048829 51048828 51048829 - TCTAAATCAATAATCAGCACAGCATGCTTCATTAACAGTGACCAATCACG "Intron (Tbc1d5-201/Tbc1d5 intron 2 of 21)" 17 50733124 51179168 446045 2 Tbc1d5-201 130339 Tbc1d5-201;Tbc1d5-207;Tbc1d5-205;Tbc1d5-208;Tbc1d5-203;Tbc1d5-202;Tbc1d5-206;Tbc1d5-209 Tbc1d5;Tbc1d5;Tbc1d5;Tbc1d5;Tbc1d5;Tbc1d5;Tbc1d5;Tbc1d5 0;0;0;0;0;0;0;0 TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE Intron 72238 ENSMUSG00000023923 conserved gene and region + TRUE EnhA6 NA no 0.983456223 0.972236071 0.993368628
cg01683044_BC21 cg01683044 Hoxc5 Hoxc5_Intron 15 102998147 102998196 102998195 102998196 - TCACAAGTTGGATTGGCCACAAGAAGTCATGTGGATTCCATCCATGAACG "Intron (Hoxc5-202/Hoxc5 intron 1 of 1)" 15 102967443 103015676 48234 1 Hoxc5-202 30704 Hoxc5-202;Hoxc6-202;Hoxc6-203;Hoxc8-201;Hoxc8-202 Hoxc5;Hoxc6;Hoxc6;Hoxc8;Hoxc8 0;0;0;0;0 TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE Intron 15424 ENSMUSG00000022485 conserved gene but different region + TRUE BivProm4 NA no 0.978218129 0.967536852 0.999052611
cg02153806_BC21 cg02153806 Dlx6 Dlx6_Exon 6 6869356 6869405 6869404 6869405 + GTCTTCAGAATGGTTTAAAACCGATCAGTCTTGTCATTTTCTAGCATTCG "Exon (Dlx6os1-201/Dlx6os1-201 exon 2 of 3)" 6 6863798 6865430 1633 1 Dlx6-204 5558 Dlx6-203;Dlx6-202;Dlx6-201;Dlx6-204 Dlx6;Dlx6;Dlx6;Dlx6 0;0;0;0 TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE Exon 13396 ENSMUSG00000029754 mapped to different genes + TRUE ReprPC1 NA no 0.986441406 0.934056314 0.974226175
cg02176373_BC21 cg02176373 Ebf3 Ebf3_fiveUTR 7 137314192 137314241 137314240 137314241 + GTTGTTGTTGTTTGCAGGCGCGCTCAACGTGGTGTCATCCTAGCCAGGCG Promoter (<=1kb) 7 137193673 137314445 120773 2 Ebf3-204 204 Ebf3-204;Ebf3-201;Ebf3-202;Ebf3-203;Ebf3-208;Ebf3-206 Ebf3;Ebf3;Ebf3;Ebf3;Ebf3;Ebf3 0;0;0;0;0;0 TRUE FALSE TRUE TRUE FALSE TRUE FALSE FALSE FALSE fiveUTR 13593 ENSMUSG00000010476 conserved gene but different region + TRUE BivProm1 NA yes 0.902322284 0.925238322 0.93821557 0.865241192
cg02187860_TC22 cg02187860 Mvb12b Mvb12b_Intron 2 33941649 33941698 33941649 33941650 - CGCAATCAGTTACTGCATTACAAGGCCGGCGATGAGCTTTTAAATCTTGG "Intron (Gm13403-201/Gm13403-201 intron 1 of 1)" 2 33729953 33887946 157994 2 Mvb12b-201 -53752 NA NA NA TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE Intron 72543 ENSMUSG00000038740 mapped to different genes NA TRUE EnhA6 NA no 0.948610266 0.782196466 0.913801589
cg02529685_TC11 cg02529685 Zfhx4 Zfhx4_Exon 3 5242361 5242410 5242409 5242410 - TTAGCAGGAGTTGGTCCTGTGTTGCACAGTTTCCGTGTCTATGATCTCCG "Exon (Zfhx4-203/Zfhx4 exon 2 of 11)" 3 5218526 5413165 194640 1 Zfhx4-203 23835 Zfhx4-203;Zfhx4-202;Zfhx4-201;Zfhx4-204;Zfhx4-205 Zfhx4;Zfhx4;Zfhx4;Zfhx4;Zfhx4 0;0;0;0;0 TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE Exon 80892 ENSMUSG00000025255 conserved gene and region + TRUE TxEnh5 NA no 0.972934528 0.991723209 0.995953629
cg02574073_BC11 cg02574073 Hoxb6 Hoxb6_Promoter 11 96292383 96292432 96292431 96292432 + GTTTATGAGTGGTTGAATCCAGCGATTGGCCGGCGCCGGTCATGTGGCCG Promoter (<=1kb) 11 96292476 96301569 9094 1 Hoxb6-202 -44 Hoxb6-202;Hoxb7-201;Hoxb7-202 Hoxb6;Hoxb7;Hoxb7 0;0;3668 TRUE FALSE TRUE FALSE FALSE FALSE TRUE FALSE FALSE Promoter 15414 ENSMUSG00000000690 mapped to different genes + TRUE BivProm4 NA yes 0.919004019 0.927113808 0.915737444 0.88134488
cg02955020_BC22 cg02955020 Pbx1 Pbx1_Exon 1 168185018 168185067 168185018 168185019 - CGCTCATGAACAAATCTCCAGAGTTTGACATGTTAAAAGAACTGGAAGAA "Exon (Pbx1-205/Pbx1 exon 7 of 9)" 1 168119364 168432270 312907 2 Pbx1-208 247203 Pbx1-208;Pbx1-205;Pbx1-206;Pbx1-201;Pbx1-202 Pbx1;Pbx1;Pbx1;Pbx1;Pbx1 0;0;0;0;0 TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE Exon 18514 ENSMUSG00000052534 conserved gene and region - TRUE Tx5 NA no 0.980793642 0.826269717 0.999727632
cg03237342_BC21 cg03237342 Tcf12 Tcf12_Intron 9 71976205 71976254 71976205 71976206 - CGCAGGTGCAACACAGCCGTGTAGCAACACACCATTTCACAGTCTATCGG "Intron (Tcf12-202/Tcf12 intron 5 of 20)" 9 71842688 72111847 269160 2 Tcf12-202 135593 Tcf12-202;Tcf12-201;Tcf12-220;Tcf12-221;Tcf12-218;Tcf12-216;Tcf12-208;Tcf12-210;Tcf12-214;Tcf12-205;Tcf12-203;Tcf12-211;Tcf12-204;Tcf12-212 Tcf12;Tcf12;Tcf12;Tcf12;Tcf12;Tcf12;Tcf12;Tcf12;Tcf12;Tcf12;Tcf12;Tcf12;Tcf12;Tcf12 0;0;0;0;0;0;0;0;0;0;0;0;0;0 TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE Intron 21406 ENSMUSG00000032228 conserved gene and region - TRUE TxEnh7 NA no 0.954762134 0.996269531 0.986922513
cg03678139_BC21 cg03678139 Foxo6 Foxo6_Intron 4 120282530 120282579 120282578 120282579 - GTTAAAAATAACCGTCTCATCTCTTTAAATTAGTCTGTCTGCAATTACCG "Intron (Foxo6-201/Foxo6 intron 1 of 1)" 4 120267079 120287349 20271 2 Foxo6-201 4770 Foxo6-201 Foxo6 0 TRUE FALSE FALSE FALSE FALSE FALSE TRUE FALSE FALSE Intron 329934 ENSMUSG00000052135 conserved gene and region + TRUE BivProm1 NA yes 0.884059672 0.938755807 0.943249875
cg04056615_TC22 cg04056615 Celf3 Celf3_Exon 3 94484297 94484346 94484297 94484298 - CGTTGCCACGGAGACTGGGCATCTGCTCCCTTTGTGCTGCCCGAGTGCCT Promoter (<=1kb) 3 94484327 94492193 7867 1 Celf3-211 0 Celf3-214;Celf3-208;Celf3-204;Celf3-215;Celf3-201;Celf3-213;Celf3-212;Celf3-207;Celf3-206;Celf3-211;Celf3-205;Celf3-209;Celf3-210;Celf3-202;Celf3-203;Riiad1-202 Celf3;Celf3;Celf3;Celf3;Celf3;Celf3;Celf3;Celf3;Celf3;Celf3;Celf3;Celf3;Celf3;Celf3;Celf3;Riiad1 0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0 TRUE FALSE TRUE FALSE FALSE TRUE TRUE FALSE FALSE Exon 78784 ENSMUSG00000028137 conserved gene but different region - TRUE DNase1 NA yes 0.986146126 0.99047615 0.999193635 0.961230046
cg04112554_BC21 cg04112554 Tcf4 Tcf4_fiveUTR 18 69593408 69593457 69593408 69593409 - CGGCCATATGGGAAAATGCAACTGAAGGAATTGTTGTGAAAAAAGGGACA Promoter (<=1kb) 18 69593413 69675730 82318 1 Tcf4-222 0 Tcf4-201;Tcf4-207;Tcf4-240;Tcf4-254;Tcf4-246;Tcf4-206;Tcf4-202;Tcf4-257;Tcf4-232;Tcf4-248;Tcf4-231;Tcf4-205;Tcf4-253;Tcf4-238;Tcf4-249;Tcf4-219;Tcf4-227;Tcf4-250;Tcf4-229;Tcf4-260;Tcf4-226;Tcf4-216;Tcf4-256;Tcf4-230;Tcf4-221;Tcf4-234;Tcf4-258;Tcf4-217;Tcf4-247;Tcf4-252;Tcf4-218;Tcf4-243;Tcf4-237;Tcf4-239;Tcf4-262;Tcf4-223;Tcf4-212;Tcf4-204;Tcf4-225;Tcf4-222;Tcf4-261;Tcf4-255;Tcf4-203;Tcf4-241;Tcf4-236;Tcf4-228;Tcf4-220;Tcf4-242 Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4;Tcf4 0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0;0 TRUE FALSE TRUE TRUE FALSE TRUE TRUE FALSE FALSE fiveUTR 21413 ENSMUSG00000053477 conserved gene and region + TRUE TSS1 NA yes 0.963095009 0.910134759 0.985273622 0.969293382
cg04138506_TC11 cg04138506 Hoxc4 Hoxc4_Exon 15 103034850 103034899 103034850 103034851 + CGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGC "Exon (Hoxc4-202/Hoxc4 exon 2 of 4)" 15 103018934 103036405 17472 1 Hoxc4-202 15916 Hoxc4-202;Hoxc4-201 Hoxc4;Hoxc4 0;0 TRUE FALSE FALSE FALSE FALSE TRUE FALSE FALSE FALSE Exon 15423 ENSMUSG00000075394 conserved gene and region - TRUE BivProm1 NA yes 0.94593827 0.943503382 0.964672965

Total number of rows: 330948

Table truncated, full table size 139749 Kbytes.




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