CHIPseq reads from rice varieties and hybrids

  • Please find below all of our CHIP-Seq data. All reads will also be deposited to the GEO database as soon as we have a complete set of tables to complement the reads (peak files, gene location etc.).  
  • Legend: 

N : O. sativa, var. Nipponbare 
K: O. sativa, var. Kasalath 
9: O. sativa, var. 93-11 

  • Sample collection:  

Each individual sample corresponds to the aerial portion of 20 seedlings, harvested at 4 days after germination and flash-frozen in liquid nitrogen. The twenty seedlings were pooled and chromatin was extracted. For each genotype, two independent biological replicates were processed. For each biological replicate, chromatin was divided into three for the following sample types: input chromatin, H3K27me3 CHIP and H3K4me3 CHIP. 

  • Bioinformatics: 

– Files denoted with a “*” were processed by Illumina’s CASAVA 1.7 pipeline. Therefore sequence qualities need to be converted to sanger format. All other files contain sanger quality scores from CASAVA 1.8 pipeline.

– Checksum are indicated as a way to insure that the file downloaded is an exact replicate of the file posted on our server. This helps ensure the download is complete and did not generate any error. The checksums provided below correspond to the uncompressed version of the file. To obtain the checksum please run one of the following commands (please note for large files this might take a little bit longer): 
– For Mac Os X, please run the following command in the terminal: “md5 filename” where filename is the name of the file you want to know the checksum 
– For Linux, please run the following command in the terminal: “md5sum filename” where filename is the name of the file you want to know the checksum 

  • Please do not hesitate to contact us with any question email
Sample Genotypes Read Length Sequence File Link File Checksum
K49 (1)50SEK4_9_1.fq.gzc13977bcaa08eb480fba5e7b84e36897
   K4_9_1-2.fq.gzc815a48f833336bc8cb1d8a573c02c6f
 9 (2)50SEK4_9_2.fq.gz03483d0192bb2275c2e0a77ddb0dfcf8
 K (1)50SEK4_K_1.fq.gz54cb7cd94870f807c9efaf3f802e38fb
   K4_K_1-2.fq.gza987b452061f4f285e3616998c0c9c69
 K (2)50SEK4_K_2.fq.gz0b7ece83d0236c60353f95b177d49d6d
 N (1)50SEK4_N_1.fq.gzb1afc052057d2b5e0e4c04109de6f0fe
 N (2)50SEK4_N_2.fq.gz5559b063c22a4ce4976abe22e972826c
   K4_N_2-2.fq.gz8da79cae0a68a3c5c0dfd59d94de3d12
 p (1)50SEK4_p_1.fq.gz4fa8b78c46b6e86d11ab1c7c5afbabe6
 p (2)50SEK4_p_2.fq.gz3c2c87792b631ecdff291abb73b4de99
   K4_p_2-2.fq.gz5d4c1a851d48be0b06e33dd5f0ea3fb6
 9K (1)50SEK4_9K_1.fq.gzf271c08d599b7a163ea5b9105dfd95bb
   K4_9K_1-2.fq.gz485c20c5bb8d546b9a64fbe3c2dd3c80
 9K (2)50SEK4_9K_2.fq.gz9b44d69bf87c763170cd7a08f1a7ba96
 K9 (1)50SEK4_K9_1.fq.gzfa8915f3d8d4171c35dbf06b28f194fb
 K9 (2)50SEK4_K9_2.fq.gz2b425999f1dd828ddbfdd647e86e9037
   K4_K9_2-2.fq.gz8ca5fd11e3783a620d76ca52e0ac9c85
 9N (1)50SEK4_9N_1.fq.gz3ccba6ae27de53695403c25268998936
   K4_9N_1-2.fq.gz5a749a327a6900268eacfa81dcc74ab0
 9N (2)50SEK4_9N_2.fq.gz4925634bfc37bae027d029618120e0a9
   K4_9N_2-2.fq.gz2cf32d9c70ec30361444eccc117c7d58
 N9 (1)50SEK4_N9_1.fq.gzd49de8bb0cb7758fbb92a52dd4de9598
   K4_N9_1-2.fq.gz190f85cfa3151478e032e8ed4282aa1b
 N9 (2)50SEK4_N9_2.fq.gze91bdbc90af4813c0e2c8d4963b5460a
   K4_N9_2-2.fq.gz067926b149a6daab76b8d7995773f706
   K4_N9_2-3.fq.gzd3285b8d93ffc8311a22c2cb0dd2731d
 KN (1)50SEK4_KN_1.fq.gz8d9bbcbbe1b5d49ba2a8f3d3618b132d
   K4_KN_1-2.fq.gz8cdf2d4624a868c0f1059a5436b2bd86
 KN (2)50SEK4_KN_2.fq.gz846475bb0cbca31e28bd4d5b61eda15f
   K4_KN_2-2.fq.gz6ca901535f9608090e19da894fff203f
 NK (1)50SEK4_NK_1.fq.gze211974225a44e9590f8f74748fad57d
   K4_NK_1-2.fq.gz7e7cfa29e170ab1a801ec95f7e4f7a4f
 NK (2)50SEK4_NK_2.fq.gz1b1fbca37866bc467109e9472628b812
   K4_NK_2-2.fq.gz5bcf9471658ee8b03dbc67dec9d16677
K279 (1)50SEK27_9_1a.fq.gz538aa048518f45e3042e292853fa096c
   K27_9_1a-2.fq.gz9bc944617db31ac11756d9ab9dd9460a
   K27_9_1b.fq.gz88b9564cc32cd999bee75dacf5958096
 9 (2)50SEK27_9_2a.fq.gzf83cc98f29e08447bb4e9bafd70998a9
   K27_9_2a-2.fq.gze7c48298dc5f76ca3ef4cef61ce308b1
   K27_9_2b.fq.gz6579e209e1487a5a3c98b7f292a47abf
   K27_9_2b-2.fq.gze03837e610e635ebbce7d4db39d02c5a
 K (1)50SEK27_K_1.fq.gz63737319731fc2803ea4463cb0450f98
 K (2)50SEK27_K_2.fq.gz58b925f8f2eb5d7dae76a3445ca0af39
  100PEK27_K_2-2-1.fq.gz1ca5b57b4c0615328d02f409e9beb50a
   K27_K_2-2-2.fq.gz75610eeefb8b9360177dad3d64c18686
 N (1)50SEK27_N_1.fq.gz33253f03848413531c30fabddbfdb2fa
  100PEK27_N_1-2-1.fq.gzd17de6858f0fa52cd5feb65b12e7e2e9
   K27_N_1-2-2.fq.gz731e7a00a3e5957e8b0c318186f6bfea
 N (2)50SEK27_N_2.fq.gz10dc7a433a17a4967f8d18ace1ca716b
 p (1)50SEK27_p_1a.fq.gzf8a2e7ccc651eb9a925132fe8bf13b8d
   K27_p_1b.fq.gz8e067ccaa35386c8acf43d57bdf4978a
 p (2)50SEK27_p_2a.fq.gzef2f3518f84e02ddf1c170f78b0a9955
   K27_p_2a-2.fq.gz67c3613eb6f001e67a5dc13e58221d43
   K27_p_2b.fq.gz5de74e6875a8236daa28efdfd2ac52bc
   K27_p_2b-2.fq.gz31af1a7521c5c659aa97c8243f762f7b
 9K (1)50SEK27_9K_1.fq.gzc7c1a21b3b97d9122a38ea42ef7ca7ec
   K27_1-2.fq.gz94781d44e5872c1a25a4f2519fbdf7b3
 9K (2)50SEK27_9K_2.fq.gza85ac4a3e9a8d7cf0df4f912521b9f95
   K27_9K-2-2.fq.gzb681e5478ebe9c0d5be2fe542d65af2e
 K9 (1)50SEK27_K9_1.fq.gz30148b67da663673529f2673460c4dd1
 K9 (2)50SEK27_K9_2.fq.gzdc6633a53ae169e00bf188a741c15435
   K27_K9_2-2.fq.gz9afdfe16847f36da7a000921247de651
 9N (1)50SEK27_9N_1.fq.gzd3d3b299eca2ae07aeb4819f6af58340
 9N (2)50SEK27_9N_2.fq.gz5b2bb98e2e6754934a39c2ef7886d141
 N9 (1)50SEK27_N9_1.fq.gzed364a235c8d2d696dd83f4079cc4c31
   K27_N9_1-2fq.gz9a7a322e9fbf2515971bebaa4d7833d8
 N9 (2)50SEK27_N9_2fq.gz8d0b3fe55c8c0f007974e051cf17485c
 KN (1)50SEK27_KN_1a.fq.gz09ee9efccd406aab3e780bdc438da353
   K27_KN_1a-2.fq.gza440b48bb6966ca9351b431a469b010f
   K27_KN_1b.fq.gz0f1f54082ae2b241a8a70ec102f73cc9
   K27_KN_1b-2.fq.gz252195a6aeb882393917ea690f852eb1
 KN (2)50SEK27_KN_2a.fq.gz4a315b8e14819f49699f19924fd80f46
  100PEK27_KN_2a-2-1.fq.gz09a65832c9b137c36645b464b3b7d6d2
   K27_KN_2a-2-2.fq.gzc5a8471c57075c2bf33fb2e76c5cbdb7
  50SEK27_KN_2b.fq.gze147af97ea33dc5cd08f435244714fc1
  100PEK27_KN_2b-2-1.fq.gz0b48720e3306a5053032a99c230cef71
   K27_KN_2b-2-2.fq.gz745ad2f198f78454f9661a5be1777934
 NK (1)50SEK27_NK_1a.fq.gza32bf034ad124c77b5055328db1b76bb
   K27_NK_1a-2.fq.gz88d31158d07890f048f6d47182d9a8d3
  100PEK27_NK_1a-3-1.fq.gz133a196fb027920540e96b6a588692b3
   K27_NK_1a-3-2.fq.gz4480668bff48f31d278f540c814d5184
  50SEK27_NK_1b.fq.gzdf2cafe1d0fcf52975b2c8e7d08146fb
   K7_NK_1b-2.fq.gz92bdd8bda709ffff0d5f321cefcc195f
  100PEK27_NK_1b-3-1.fq.gz625e1e9ab6be9bd3fdf38877a526ed34
   K27_NK_1b-3-2.fq.gz647a5931f1f483806e4cd3691a2275b2
 NK (2)50SEK27_NK_2a.fq.gzf613d3ce8ab6e453cc63611ee2539d7f
   K27_NK_2b.fq.gz5d6408facbd3961e99302ec11810a07a
Input *9 (1)50SEInput_9_1.fq.gzbb47bc63d04eac9acafb3921173eb974
 9 (2)50SEInput_9_2.fq.gzc25387ad0968f564f5a40ddd21722ea4
 K (1)50SEInput_K_1.fq.gz522ef13424c895496bf572d8827037ac
 K (2)50SEInput_K_2.fq.gzf98cc11193c571c1300446026bcc30c0
 N (1)50SEInput_N_1.fq.gz4271dd7223f9f8e014d965203fd8b0e5
 N (2)50SEInput_N_2.fq.gz0d7530dbb8515555b7758e09dc8380b2
 p (1)50SEInput_p_1.fq.gzcc5298cf473ddc3cd71ef3c97ce4c5d6
 p (2)50SEInput_p_2.fq.gz5808291d9e4e800f6f2030395ff3a4ac
 9K (1)50SEInput_9K_1.fq.gz305c78564cdbf1208fd08c502eeb82bf
 9K (2)50SEInput_9K_2.fq.gz5f73e33e7888c47a7ea4ba851db71e22
 K9 (1)50SEInput_K9_1.fq.gzb5926e5ae75425765d3c8ff97ed24ad9
 K9 (2)50SEInput_K9_2.fq.gz036e5a68d1ee4b506179a4d6872c1519
 9N (1)50SEInput_9N_1.fq.gzfcfb3e3b81f4d63ef2b52b9201ddc8b1
 9N (2)50SEInput_9N_2.fq.gz9e3167a0a1edce55c0b09b3b0660437a
 N9 (1)50SEInput_N9_1.fq.gzb650258c8a0f8031bba8337a47de77b2
 N9 (2)50SEInput_N9_2.fq.gzf04733215ad233154bc746c4b0994a0d
 KN (1)50SEInput_KN_1.fq.gz2b6a21d99ffd8907e9402993ea46ad58
 KN (2)50SEInput_KN_2.fq.gzcbd04cb5d8bbf428765632e67023dd7f
 NK (1)50SEInput_NK_1.fq.gz35313a89463775b9ff545c4d0a93a1e5
 NK (2)50SEInput_NK_2.fq.gza4f979078f2cd68ee8940413a13e4bba
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