Data contents

Number of dataset Data contents
  Human Mouse Malaria Chyzon Rat Chimpanzee Macaque
TSS-seq 73 7 1 1 1 1 2
RNA-seq 42 36 0 0 0 0 0
ChIP-seq 255 162 0 0 0 0 0
RIP-seq 12 6 0 0 0 0 0
BS-seq 26 16 0 0 0 0 0
ChromHMM 36 0 0 0 0 0 0
SNV 49 0 0 0 0 0 0
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Dataset table Data contents
Human
  Lung cancer
26 cell-lines		 Other cancer
cell-lines		 Normal
cell-lines		 Normal
tissues		 Clinical samples
(ICGC, TCGA, etc.)
TSS-seq ♦ ♦ -
RNA-seq total RNA ♦ ♦ ♦ - -
polysome - - -
nucleosome -
cytoplasmic -
ChIP-seq
(transcription factor)		 Pol II ♦ ♦ - -
HIF1A - -
STAT6 -
ChIP-seq
(histone modification)		 H3K27me3 ♦ ♦ - -
H3K4me3 -
H3ac -
H3K27ac - -
H3K36me3 -
H3K4me1 -
H3K9me3 -
Bisulfite sequencing ♦ - -
SNV ♦ - ♦

Mouse
  3T3 10T1/2 embryo ATDC5
TSS-seq ♦
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Clinical samples Data contents
 
Data provider Disease type Number of samples Reference
National Cancer Center Hospital East and University of Tokyo Lung adenocarcinoma 97 PLoS One. 2013 Sep 12;8(9):e73484.
National Cancer Center Hospital East Small cell lung cancers 57 J Thorac Oncol. 2014 Sep;9(9):1324-31.
ICGC 43 of ICGC DCC Project Codes 6,590 https://dcc.icgc.org/
Dr. Meyerson's Lab. Lung adenocarcinoma 183 Cell. 2012 Sep 14;150(6):1107-20.
Dr. Ogawa's Lab. Myelodysplasia 29 Nature. 2011 Sep 11;478(7367):64-9
Clear-cell renal cell carcinoma 106 Nat Genet. 2013 Aug;45(8):860-7
TCGA Gastric adenocarcinoma 295 Nature. Published online 23 July 2014
Urothelial bladder carcinoma 131 Nature. 507 (7492):315-22.
Glioblastoma 291 Cell. 155 (2):462-477.
Clear cell renal cell carcinoma 446 Nature. 499 (7456):43-49.
Endometrial carcinoma 373 Nature. 497 (7447):67-73.
Acute myeloid leukemia 200 NEJM. 368:2059-2074.
Breast tumors 507 Nature. 490 (7418):61-70.
Squamous cell lung cancers 178 Nature. 489 (7417):519:525.
Colon and rectal cancer 224 Nature. 487 (7407):330-337.
Ovarian carcinoma 316 Nature. 474 (7353):609-615.
Glioblastoma 91 Nature. 455 (7216):1061-1068.
HGVD Normal (Japanese) 1,208 URL: http://www.genome.med.kyoto-u.ac.jp/SnpDB
ToMMo Normal (Japanese) 1,070 URL: http://humandbs.biosciencedbc.jp/en/hum0015-v1
JPDSC (Japan PGx Data Science Consortium) Normal (Japanese) 2,994 URL: http://humandbs.biosciencedbc.jp/hum0013-v1
ExAC Various disease 60,706 URL: http://exac.broadinstitute.org/
Total 76,092  
 
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Cell lines Data contents
 
Cell line General information* Cell culture Sequencing dataset Memo
Name Type in-house analysis number Distributor Catalogue number Ethnicity Gender Age Smoking status Medium Dish Whole-genome RNA-Seq BS-Seq ChIP-Seq** TSS-Seq
SAEC (control) Small airway epithelial cell s_35 TAKARA (Lonza) - - M - - - collagen Type I-coated - ♦ - ♦ ♦ Normal
PC-9 lung adenocarcinoma s_9 RIKEN BRC RCB4455 Japanese - - - RPMI - ♦ ♦ ♦ ♦ ♦ -
PC-14 lung adenocarcinoma s_10 IBL - Japanese - - - RPMI - ♦ ♦ ♦ ♦ ♦ -
RERF-LC-KJ lung adenocarcinoma s_13 RIKEN BRC RCB1313 Japanese M 78 - RPMI - ♦ ♦ ♦ ♦ ♦ -
RERF-LC-Ad1 lung adenocarcinoma s_11 JCRB JCRB1020 Japanese M 70 - RPMI - ♦ ♦ ♦ ♦ ♦ -
RERF-LC-Ad2 lung adenocarcinoma s_12 JCRB JCRB1021 Japanese M - - RPMI - ♦ ♦ ♦ ♦ ♦ -
LC2/ad lung adenocarcinoma s_18 RIKEN BRC RCB0440 Japanese F 51 - DMEM collagen Type I-coated ♦ ♦ ♦ ♦ ♦ -
RERF-LC-MS lung adenocarcinoma s_14 JCRB JCRB0081 Japanese - - - EMEM - ♦ ♦ ♦ ♦ ♦ -
VMRC-LCD lung adenocarcinoma s_16 JCRB JCRB0814 Japanese M - - EMEM - ♦ ♦ ♦ ♦ ♦ -
ABC-1 lung adenocarcinoma s_17 JCRB JCRB0815 Japanese M 47 - EMEM - ♦ ♦ ♦ ♦ ♦ -
PC-7 lung adenocarcinoma s_8 IBL - Japanese - - - RPMI - ♦ ♦ ♦ ♦ ♦ Non-adherent
PC-3 lung adenocarcinoma s_7 JCRB JCRB0077 Japanese F 48 - RPMI collagen Type I-coated ♦ ♦ ♦ ♦ ♦ -
II-18 lung adenocarcinoma s_19 RIKEN BRC RCB2093 Japanese - - - RPMI - ♦ ♦ ♦ ♦ ♦ -
RERF-LC-OK lung adenocarcinoma s_15 JCRB JCRB0811 Japanese - - - RPMI - ♦ ♦ ♦ ♦ ♦ -
A549 lung adenocarcinoma s_1 ATCC CCL-185 Caucasian M 58 - DMEM - ♦ ♦ ♦ ♦ ♦ -
A427 lung adenocarcinoma s_20 ATCC HTB-53 Caucasian M 52 - RPMI - ♦ ♦ ♦ ♦ ♦ -
H322 lung adenocarcinoma s_21 ATCC CRL-5806 Caucasian - - - RPMI - ♦ ♦ ♦ ♦ ♦ -
H1648 lung adenocarcinoma s_25 ATCC CRL-5882 Black M 39 Y RPMI collagen Type I-coated ♦ ♦ ♦ ♦ ♦ -
H1650 lung adenocarcinoma s_26 ATCC CRL-5883 Caucasian M 27 Y RPMI - ♦ ♦ ♦ ♦ ♦ -
H1975 lung adenocarcinoma s_29 ATCC CRL-5908 - F - N RPMI - ♦ ♦ ♦ ♦ ♦ -
H1299 lung adenocarcinoma s_23 ATCC CRL-5803 Caucasian M 43 - RPMI - ♦ ♦ ♦ ♦ ♦ -
H2228 lung adenocarcinoma s_22 ATCC CRL-5935 - F - N RPMI - ♦ ♦ ♦ ♦ ♦ -
H1819 lung adenocarcinoma s_28 ATCC CRL-5897 Caucasian F 55 Y RPMI - ♦ ♦ ♦ ♦ ♦ -
H2126 lung adenocarcinoma s_30 ATCC CCL-256 Caucasian M 65 - RPMI - ♦ ♦ ♦ ♦ ♦ BL2126 (Counterpart, B lymphoblast)
H2347 lung adenocarcinoma s_31 ATCC CRL-5942 Caucasian F 54 N RPMI collagen Type I-coated ♦ ♦ ♦ ♦ ♦ BL2347 (Counterpart, B lymphoblast)
H1703 lung adenocarcinoma s_27 ATCC CRL-5889 Caucasian M 54 Y RPMI - ♦ ♦ ♦ ♦ ♦ -
H1437 lung adenocarcinoma s_24 ATCC CRL-5872 Caucasian M 60 Y RPMI - ♦ ♦ ♦ ♦ ♦ BL1437 (Counterpart, B lymphoblast)
 
* Refer to the Distributors' web pages; IBL: Immuno-Biological Laboratories; JCRB: Japanese Collection of Research Bioresources; RIKEN BRC: RIKEN Bio Resource Center; ATCC: American Type Culture Collection. ** Eight chromatin marks (H3K4me3, H3K9/14ac, H3K36me3, Pol II, H3K4me1, H3K27ac, H3K27me3, H3K9me3)
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Contents of statistics Data contents
  [26 cell lines of lung cancer]
Table 1-1. Statistics of the TSS-seq
Table 1-2. Statistics of the RNA-seq
Table 1-3. Statistics of the SNVs
Table 1-4. Statistics of the whole-genome sequencing
Table 1-5. Statistics of the ChIP-seq
Table 1-6. Statistics of the bisulfite sequencing
Figure 1-1. Validation about replicates
Figure 1-2. Comparison with ENCODE data

[Other culture cells]
Table 2-1. Statistics of the TSS-seq
Table 2-2. Statistics of the RNA-seq
Table 2-3. Statistics of the ChIP-seq
Table 2-4. Statistics of the TSS-seq (mouse)

[Accession numbers]
  
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Statistics of TSS-seq Data contents
 
Table 1-1. Summary of the TSS-seq data.
Cell line Used sequences
(Read1)		 Num of genes
> 1 ppm > 5 ppm
PC-3 18,649,350 11,785 8,990
PC-7 16,060,356 11,770 8,784
PC-9 11,130,325 12,063 8,660
PC-14 19,534,562 11,899 9,072
RERF-LC-Ad1 48,239,845 12,659 9,899
RERF-LC-Ad2 11,764,859 12,909 10,376
RERF-LC-KJ 73,852,979 12,289 9,647
RERF-LC-MS 79,069,291 13,385 10,394
RERF-LC-OK 24,754,476 11,931 8,867
VMRC-LCD 4,872,185 11,664 9,256
ABC-1 34,614,777 11,492 8,748
LC2/ad 25,279,212 12,243 9,178
II-18 21,167,116 11,575 8,854
A549 42,592,864 11,829 8,710
A427 54,220,585 11,669 9,087
H322 38,669,256 12,400 9,917
H2228 19,845,847 12,085 8,996
H1299 20,724,948 11,482 8,946
H1437 46,833,660 12,441 9,880
H1648 33,847,057 12,594 9,691
H1650 26,429,904 12,679 10,080
H1703 47,880,972 11,317 8,587
H1819 24,589,847 12,458 9,709
H1975 13,770,088 12,407 9,641
H2126 75,840,941 12,116 9,613
H2347 16,793,926 12,093 9,219
 
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Statistics of RNA-seq Data contents
 
Table 1-2. Summary of the RNA-seq data.
Cell line Used sequences
(Read1)		 Num of genes
> 1 RPKM > 5 RPKM
PC-3 49,914,547 12,205 9,240
PC-7 50,925,975 12,129 9,009
PC-9 34,167,521 12,817 9,532
PC-14 53,977,381 12,169 9,037
RERF-LC-Ad1 56,406,046 12,298 9,206
RERF-LC-Ad2 45,580,359 12,392 8,804
RERF-LC-KJ 60,803,665 12,054 8,938
RERF-LC-MS 52,715,099 13,045 9,090
RERF-LC-OK 33,086,988 12,309 8,954
VMRC-LCD 45,944,953 12,502 8,711
ABC-1 37,993,504 11,715 8,384
LC2/ad 43,665,988 12,366 9,206
II-18 63,869,445 11,955 9,038
A549 20,440,396 12,155 8,998
A427 41,895,881 11,866 9,011
H322 54,487,583 12,457 9,351
H2228 56,465,940 12,409 9,106
H1299 51,120,991 11,735 8,958
H1437 49,890,034 12,275 8,921
H1648 38,908,100 12,604 9,317
H1650 26,635,691 12,716 9,595
H1703 87,705,180 11,736 8,695
H1819 75,262,673 12,494 9,185
H1975 36,195,247 12,715 9,634
H2126 46,862,796 12,143 9,016
H2347 50,325,156 12,278 9,030
SAEC 180,054,144 12,126 8,809
 
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Statistics of the SNVs Data contents
 
Table 1-3. The number of SNVs and short indels in the 26 cell lines.
  Total number of positions (Avg. of the 26 cell lines)
SNVs Short indels SNVs Short indels
Total 12,732,271 1,916,622 (3,302,407) (453,821)
  Germline 10,010,429 1,597,810 (3,177,173) (429,846)
  Somatic candidates 2,721,842 318,812 (125,234) (23,975)
    Genic∗ 892,941 118,268 (39,695) (8,516)
      Upstream (-500 from TSS) 11,796 2,049 (551) (159)
      UTRs 24,902 13 (1,086) (0.8)
      CDS 16,354 573 (687) (37)
        Synonymous 4,505 ∗∗∗ (188) ∗∗∗
        Non-synonymous 11,849 ∗∗∗ (499) ∗∗∗
      Splice sites† 346 39 (14) (3)
      Intronic and others 839,543 115,594 (37,357) (8,315)
    Intergenic 1,828,901 200,544 (85,539) (15,459)
∗ A total of 19,958 genes were used in this analysis.
† The first and last two bases in introns.
 
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Statistics of WGS Data contents
 
Table 1-4. Summary of the whole-genome sequencing data.
  Mapped sequences
(Read1+Read2)		 Depth (avg) Coverage (x5)
PC-7 1,181,752,959 38.4 0.92
PC-9 1,235,410,075 40.2 0.91
PC-14 1,377,953,696 44.8 0.91
RERF-LC-ad1 1,189,406,566 38.7 0.91
RERF-LC-ad2 1,204,958,194 39.2 0.92
RERF-LC-KJ 1,058,371,222 34.4 0.92
RERF-LC-MS 1,234,238,416 40.2 0.92
RERF-LC-OK 677,038,144 21.8 0.91
VMRC-LCD 1,270,060,339 41.3 0.91
ABC-1 1,131,071,585 36.8 0.91
LC2/ad 1,265,338,449 41.2 0.91
II-18 860,643,037 27.6 0.90
A549 723,563,287 22.2 0.86
A427 1,040,002,036 33.8 0.91
H322 893,332,828 28.9 0.90
H2228 830,781,519 27.0 0.91
H1299 899,909,551 29.3 0.91
H1437 711,909,693 23.1 0.91
H1648 1,065,042,096 34.6 0.92
H1650 1,031,008,238 33.5 0.91
H1703 984,465,974 31.6 0.91
H1819 1,091,791,039 35.5 0.91
H1975 1,004,161,315 32.6 0.91
H2126 640,653,382 20.8 0.91
H2347 948,973,026 30.9 0.91
 
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Statistics of ChIP-seq Data contents
 
Table 1-5. Summary of ChIP-seq.
  Average of mapped
sequences		 Average of number of peaks (MACS2)
Narrow peaks Broad peaks
H3K4me3 26,140,455 21,209 16,208
H3K9/14ac 19,596,187 34,374 23,753
Pol II 26,056,772 15,715 13,997
H3K36me3 24,264,604 107,708 47,710
H3K4me1 25,900,257 108,882 75,854
H3K27ac 25,690,276 61,061 38,297
H3K27me3 21,584,812 53,587 42,163
H3K9me3 21,155,573 39,559 51,760
WCE 19,100,553 ∗∗∗ ∗∗∗
 
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Statistics of bisulfite-seq Data contents
 
Table 1-6. Summary of bisulfite sequencing data.
Cell line Mapped
sequences		 Avg. of depths Conversion rate
(x5)∗		 CpG sites (> x5)
PC-3 157,902,653 161.4 0.994 3,673,159
PC-7 109,919,011 110.9 0.994 3,418,929
PC-9 87,012,056 89.6 0.994 3,231,320
PC-14 204,216,479 210.3 0.994 4,064,068
RERF-LC-Ad1 87,043,746 89.1 0.992 3,264,395
RERF-LC-Ad2 78,300,691 83.0 0.994 3,448,211
RERF-LC-KJ 72,844,738 74.9 0.993 3,068,971
RERF-LC-MS 102,938,936 109.0 0.994 3,598,662
RERF-LC-OK 161,552,507 165.0 0.993 3,758,532
VMRC-LCD 84,681,570 89.5 0.992 3,136,774
LC2/ad 112,097,386 116.0 0.988 3,548,548
ABC-1 93,158,547 93.1 0.993 3,493,903
II-18 99,682,438 165.0 0.993 3,327,001
A549 87,966,180 91.0 0.991 3,324,364
A427 53,499,542 54.3 0.992 2,614,641
H322 153,896,186 165.8 0.989 4,161,775
H2228 122,705,759 81.6 0.993 4,815,543
H1299 118,923,875 82.2 0.994 4,533,930
H1437 98,311,209 63.1 0.993 4,382,225
H1648 102,033,841 104.4 0.989 3,357,747
H1650 105,694,196 109.4 0.994 3,460,378
H1703 127,897,486 81.6 0.994 5,513,896
H1819 220,008,485 223.4 0.986 4,085,231
H1975 79,688,628 81.7 0.993 3,274,116
H2126 124,651,437 80.2 0.993 4,991,289
H2347 115,973,241 76.1 0.993 4,661,415
∗ Conversion rate: (TA+TT+TC) / (CA+CT+CC+TA+TT+TC).
 
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Replicates Data contents
 
Figure 1-1. Replicates of ChIP-seq data.
Intensity = [ChIP PPM] / [WCE PPM] (∗ ± 1.5 kb from TSS)
r: Pearson correlation coefficient 		 
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Comparison of ChIP-seq data Data contents
 
Figure 1-2. Comparison of ChIP-Seq data between our dataset and ENCODE project.
  
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Statistics of TSS-seq Data contents
 
Table 2-1. Summary of the TSS-seq data.
Cell line Average of
used sequences (Read1)		 Average of number of genes
> 1 ppm > 5 ppm
DLD-1 8,096,747 11,405 8,205
MCF7 7,892,874 11,025 7,694
HEK293 10,343,055 11,193 7,788
Ramos 15,511,412 10,278 7,445
Hela 1,533,369 11,822 8,526
TIG3 9,390,005 11,198 7,959
Beas2B 12,344,901 11,293 7,886
Adult tissues 7,308,543 13,229 9,265
Fetal tissues 8,348,654 13,434 9,768
 
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Statistics of RNA-seq Data contents
 
Table 2-2. Summary of the RNA-seq data.
Cell line Average of
used sequences (Read1)		 Average of number of genes
> 1 RPKM > 5 RPKM
DLD-1 21,748,111 11,215 8,283
HEK293 5,798,457 12,426 9,258
Ramos 7,215,816 10,659 8,059
TIG3 16,666,416 11,645 8,400
Beas2B 27,099,590 11,758 9,081
 
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Statistics of ChIP-seq Data contents
 
Table 2-3. Summary of the ChIP-seq data. (hg19)
  21% 1%
IP total WCE total Peak IP total WCE total Peak
DLD-1 Pol II 14,397,292 19,133,214 12,405 16,431,596 17,512,096 17,512,096
H3ac 11,545,404 11,430,778 16,869 12,406,376 11,049,033 21,414
H3K4me3 15,126,753 19,803,256 27,197 14,673,411 15,244,721 29,693
H3K27me3 9,796,488 15,762,543 1,434 8,230,411 14,789,992 1,562
MCF7 Pol II 9,744,263 20,224,021 25,188 9,709,791 12,724,278 19,311
HIF1A 25,763,246 18,197,242 94,085 19,390,075 17,154,571 107,589
HEK293 Pol II 10,086,952 5,772,027 27,895 - - -
TIG3 Pol II 20,068,484 16,048,237 8,525 9,078,433 8,178,309 7,443
H3ac 11,610,062 14,092,706 10,818 10,541,222 13,273,725 7,941
H3K4me3 10,177,529 19,487,961 31,549 9,438,915 16,891,626 25,720
H3K27me3 12,207,120 14,020,038 9,035 11,616,140 17,176,075 14,968
HIF1A 18,092,915 14,732,632 13,782 16,467,590 15,541,811 674
  IL4+ IL4-
IP total WCE total Peak IP total WCE total Peak
Ramos Pol II 7,192,077 2,786,371 17,426 8,605,893 3,299,301 19,233
H3ac 31,342,754 27,241,289 51,325 37,442,045 27,794,747 35,708
H3K4me3 36,933,113 24,593,765 27,347 36,933,113 24,593,765 26,105
STAT6 4,684,426 5,008,189 600 4,550,900 4,842,993 73
Beas2B Pol II 6,869,914 3,188,421 13,453 7,911,582 3,724,882 8,171
H3ac 35,939,360 26,678,038 37,462 32,576,988 29,388,072 32,767
H3K4me3 33,520,360 27,485,630 24,264 29,914,406 26,630,062 23,466
STAT6 4,886,971 3,188,421 772 7,154,872 3,724,882 314
 
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Statistics of TSS-seq (mouse) Data contents
 
Table 2-4. Summary of the TSS-seq data (mouse).
Cell line Average of
used sequences (Read1)		 Average of number of genes
> 1 ppm > 5 ppm
NIH3T3 20,246,164 11,335 8,469
10T1/2 0h 5,084,760 9,357 6,086
ATDC5 0h 6,157,514 10,906 7,708
Embryo 9,724,446 13,114 9,585
 
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Accession numbers Data contents
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Sample name Accession
number		 Description / Catalog No. Reference
SAEC (Normal Human Small Airway Epithelial Cell): RNA-Seq and ChIP-Seq DRA002311   A. Suzuki et al., NAR, 2014
Lung cancer 26 cell-lines: Bisulfite sequencing DRA001841   A. Suzuki et al., NAR, 2014
Lung cancer 26 cell-lines: RNA-seq DRA001846
Lung cancer 26 cell-lines: Whole-genome sequencing DRA001859
Lung cancer 26 cell-lines: ChIP-seq DRA001860
Normal 3 cell-lines: Whole-genome sequencing DRA001858   A. Suzuki et al., NAR, 2014
DLD1 (Hypoxia with non-tagged RNAi) SRA003625DLD-1 cells were cultured in DME, 10% FCS under 21% or 1% O2. Cells were harvested 24 hr after the hyposic shock. Cells were also tranfected 24 hr prior to the hypoxic shock by siRNA of non-targetting RNA, HIF1A-targetting RNA or HIF2A targetting RNA. Tanimoto et al., HUGO J, 2011
DLD1 (Hypoxia with HIF1A RNAi)SRA003625
DLD1 (Normoxia with HIF1A RNAi)SRA003625
DLD1 (Hypoxia with HIF2A RNAi)SRA003625
DLD1 (Normoxia with non-targetedRNAi)SRA003625
DLD1 (Normoxia with HIF2A RNAi)SRA003625
Beas2B overexpress STAT6 IL4+ SRA008161 Beas2B cells were cultured in DME, 10% FCS. Cells were harvested 24 hr after the stimulation of 50ng/ml of IL4. Kanai et al., DNA Res., 2011
Beas2B overexpress STAT6 IL4-SRA008162
Beas2B parent IL4+DRA000017
Beas2B parent IL4-DRP000018
Beas2B STAT6 siRNA- IL4+DRA000021
Beas2B STAT6 siRNA-DRA000022
Beas2B STAT6 siRNA+ IL4+DRA000019
Beas2B STAT6 siRNA+DRA000020
Ramos IL4+ SRA008163 Ramos cells were cultured in RPMI, 10% FCS. Cells were harvested 24 hr after the stimulation of 50ng/ml of IL4.  
Ramos IL4-SRA008164
MCF7 O2 21% SRA003625 MCF7 cells were cultured in DME, 10% FCS under 21% or 1% O2. Cells were harvested 24 hr after the hyposic shock. Tsuchihara et al., NAR, 2009
MCF7 O2 1%SRA003625
TIG O2 21% SRA003625TIG-3 cells were cultured in DME, 10% FCS under 21% or 1% O2. Cells were harvested 24 hr after the hyposic shock. Tsuchihara et al., NAR, 2009
TIG O2 1%SRA003625
HEK293 O2 21% SRA003625 293 cells were cultured in DME, 10% FCS under 21% or 1% O2. Cells were harvested 24 hr after the hyposic shock. Tsuchihara et al., NAR, 2009
HEK293 O2 1%SRA003625
Hela   HeLa cells were obtained from ATCC and cultured in DME, 10% FCS.  
Fetal Heart DRA000024 Total RNA was purchased from Clontech and used for the library construction. 636526, 636529, 636530, 636532, 636583, and 636584 Yamashita et al., Genome Res., 2011
Fetal KidneyDRA000025
Fetal Liver 
Fetal Thymus 
Fetal BrainDRA000023
BrainDRA000026
HeartDRA000027
KidneyDRA000028
Adipose Total RNA was purchased from Ambion and used for the library construction.AM7956 
Adrenal AM7956
Brain AM7962
Brain2  
Breast Bio Chain R1234086-50
Colon Bio Chain R1234090-50
Heart AM7966
Kidney AM7976
Liver AM7960
Lung AM7968
Lymph AM7894
Muscle AM7982
Ovary AM6974
Prostate AM7988
Testis AM7972
Thyroid AM6872
NIH3T3 NIH3T3 cells were obteind from ATCC and cultured in DME, 10% FCS. 
Mouse embryo 7d Total RNA was purchased from Ambion and used for the library construction.Wijaya et al., Genome Inform., 2009
Mouse embryo 11d 
Mouse embryo 15d 
Mouse embryo 17d 
10T1/2 0h 10T1/2 cells were cultured in a standard condition. 
ATDC5 0h ATDC5 cells were cultured in a standard condition. 
siRNA1 controlDRA000591 Tani et al., RNA Biol., 2012
siRNA2 controlDRA000591
siRNA1 UPF1DRA000591
siRNA2 UPF2DRA000591
ChIP-seq Th1,TH2 anti-Chd4DRA000928 Hosokawa H. et al., Proc Natl Acad Sci USA., 2013
TSS-seq Th1,Th2DRA000928
ChIP-seq Th1,TH2 Ab GSE51079,SRP007894
ChIP-seq Th1,TH2 GATA3GSE51079,SRP007894
ChIP-seq Th1,TH2 H3K27me3,H3K9ac,H3K4me3GSE51079,SRP007894
ChIP-seq 3xFlag-GATA3DRA001102 Hosokawa H. et al., Proc Natl Acad Sci USA., 2013
RNA-seq Th1,Th2DRA001102
ChIP-seq Mouse Liver 1D4DRA001050 Yoshitane H. et al., Mol Cell Biol., 2014
ChIP-seq Mouse Liver CLSP4DRA001050
RNA-seq Mouse LiverDRA001050
micro RNA-seq Mouse Liver DRA001050
RNA-seq Bmap Ko Mouse LiverDRA001278
RNA-seq WT Mouse Liver DRA001278
ChIP-seq Th1,Th2 AbGSE51079 Tumes DJ. et al., Immunity., 2013
ChIP-seq Th1,Th2 Ezh2GSE51079
Reg1[-/-] LPS stimulated DRA003234 Mino T. et al., Cell., 2015
Roquin [San/San] LPS stimulatedDRA003234
TP3_wild_H3K27me3DRA000485 Tanaka S. et al., Blood., 2012
TP3_KO_H3K27me3DRA000486
MLL_AF9_AML_Ezh2_WT_inputDRA000487
TP3_4_input DRA000488
Tet2 KDDRA000858
Ezh2 KDDRA000858
Tet2 Ezh2 KD DRA000858 Muto T. et al., J Exp Med., 2013
BlastocystDRA000484 Kobayashi H. et al., PLoS Genet., 2012
ESCDRA000484
GV_oocyte_Dnmt3LDRA000484
GV_oocyte_wildDRA000484
SpermDRA000484
10.5 female PGCDRA000607 Kobayashi H. et al., Genome Res., 2013
10.5 male PGCDRA000607
13.5 female PGCDRA000607
13.5 male PGCDRA000607
16.5 female PGCDRA000607
16.5 male PGCDRA000607
CD4T TcellGSE73825 Onodera A. et al., Mol Cell Biol., 2015
B cellGSE73825
ES cellGSE73825
Th1 cellGSE73825
Th2 cellGSE73825
HBZ AcH3DRA003229 Yasuma K. et al., PLoS Pathog., 2016
HBZ IgGDRA003229
HBZ inputDRA003229
mock AcH3DRA003229
mock IgGDRA003229
mock inputDRA003229
HBZ H3K18DRA003229
HBZ H3K27DRA003229
HBZ H3K9DRA003229
HBZ inputDRA003229
HBZ isotypeDRA003229
mock H3K18DRA003229
mock H3K27DRA003229
mock H3K9DRA003229
mock inputDRA003229
mock isotypeDRA003229
HBZ_Flag_ChIPseqDRA003744
HBZ_Flag_input_DNADRA003744
RNAseq HBZ DRA003229
RNAseq primary HBZ DRA003229
RNAseq mockDRA003229
RNAseq primary mock DRA003229
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