Rice RNA-Seq Sequence Files

  • Please find below all of our RNA-Seq data. All reads will also be deposited to the GEA database as soon as we have a complete set of tables to complement the reads (read counts / transcripts, fold change etc).  
  • Legend: 

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

  • Sample collection:  

Each individual sample corresponds to the aerial portion of 5 seedlings, harvested at 4 days after germination. The five seedlings were pooled and RNA was extracted. For each genotype, three independent biological replicates were processed, with the exception of Nipponbare, for which five biological replicated were processed.

  • Bioinformatics: 

– Files denoted with a “*” were processed by Illumina’s CASAVA 1.8 pipeline. Therefore sequence qualities are already in sanger format. All other files contain quality scores inIllumina format 

– Checksum is method to check to make sure the file downloaded is the exact file you wanted to download. This also helps ensure the download is complete. The checksums provided below are for 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
Genotypes Read Length Sequence File Link File Checksum
Nipponbare(1)80 PENipponbare_1_F.txt.gze67bf48ae23812517c560754518bef83
  Nipponbare_1_R.txt.gz077b1b85f4c9a54f94d7046cbb543350
Nipponbare(2)80 PENipponbare_2_F.txt.gz81bf61110db0c8586af0d490fd83ad85
  Nipponbare_2_R.txt.gzd301cb5501b3486a68b2c642b88a9f1d
Nipponbare(3)80 PENipponbare_3_F.txt.gz28b6d7b730962ba08d1980656ba3b2d7
  Nipponbare_3_R.txt.gzd0f39b4323f92e64dad537d82deda2ee
  Nipponbare_3_F_BGI-5.txt.gz*5d04bb9a127aeb2e523083a19b181a4d
  Nipponbare_3_R_BGI-5.txt.gz*dc0cdeb6a011d0a89eb52ea6e054872b
  Nipponbare_3_F_BGI-6.txt.gz*f89156501a8c06bb2c642ac3095c2ce7
  Nipponbare_3_R_BGI-6.txt.gz*b2ef2c0b2c64970f9df0e8882fd9b4b9
Nipponbare(4)80 PEN_4_F.txt.gz*74674d72ba76a3cd403f50a7016cb646
  N_4_R.txt.gz*8970e75163b308b012cef2c98f3ca374
Nipponbare(5)80 PEN_5_F.txt.gz*82a9b6732e2ffcbd478d4ecebf231633
  N_5_R.txt.gz*d1244e0796738281b1ae7040674fea81
Kasalath(1)80 PEKasalath_1_F.txt.gz7aa2986e5b8ea01e7432acbf5dbe4028
  Kasalath_1_R.txt.gz18c12cf4c1584be730662029a25b7160
  Kasalath_1_F_BGI-5.txt.gz0bf0497447eb2bed224575fcf6c1b24f
  Kasalath_1_R_BGI-5.txt.gz653940c102c414059143f61af960299f
  Kasalath_1_F_BGI-6.txt.gzd19cfc9405d6e6967298205e0584ff3d
  Kasalath_1_R_BGI-6.txt.gz43599cdc8e2a0afab24ebb7a0bf13c0d
Kasalath(2)80 PEKasalath_2_F.txt.gzf361347bc43caa296479cdb31ad52a9f
  Kasalath_2_R.txt.gz0b49f6ed3a38bc1c8123afa828d38ce7
  Kasalath_2_F_BGI-5.txt.gz82c4ae0767032de6adeca2bab8d7ddcb
  Kasalath_2_R_BGI-5.txt.gz96b2e0fb25103c01f3722a3cde5be0f9
  Kasalath_2_F_BGI-6.txt.gz981c210bfdcab9d2267cc3e066441ca9
  Kasalath_2_R_BGI-6.txt.gzb56c1329b32acbc1ff0a384291d54033
Kasalath(3)80 PEKasalath_3_F.txt.gzbaa30c230c48ee1c6270a498eaee21e4
  Kasalath_3_R.txt.gzb6d11922a3540f271c7d5c7e9138f13d
  Kasalath_3_F_BGI-5.txt.gzc55cb0a899fbba091a2c6c363b11fa18
  Kasalath_3_R_BGI-5.txt.gzd0b55ba6c4c0b051c996bf6eb9c71975
  Kasalath_3_F_BGI-6.txt.gz508f76ac75875e4552c2b19502538572
  Kasalath_3_R_BGI-6.txt.gz3df30d5cd651e683d1e09477b76dd705
punctata (1)80 PEpunctata_1_F.txt.gz 8c5cc918b06a3cdcdef3e6838efb67cc
  punctata_1_R.txt.gz 938c1b09405e4fe671db34f5d239bda7
punctata (2)80 PEpunctata_2_F.txt.gz2ced28b30591378e97572e02e4035f55
  punctata_2_R.txt.gz8b287f419fd2b698ca9df871ee08647b
punctata (3)80 SRpuncatata_3_80SR.txt.gz f85ad45873fbb0002a3ccf3c6a85803d
N x K (1)80 PENxK_1_F_BGI-5.txt.gzce3b70e669096e83ac4b2d9198b504dd
  NxK_1_R_BGI-5.txt.gzb2e9e7424581271e3121c6dcd497b9f9
  NxK_1_F_BGI-6.txt.gz640613154a1a24c3505da4690cc7dfe2
  NxK_1_R_BGI-6.txt.gz1094a299cc12468f87d2d21f29ba1417
 N x K (1)80 SRNxK_1_80SR.txt.gz0ea5af156b2887554b563bde1404ae29
N x K (2)80 PENxK_2_F_BGI-5.txt.gzcc0e08e665f6df373ad5beeb48cd7752
  NxK_2_R_BGI-5.txt.gz1e27f0f53f600736eeb17d9468baa6c5
  NxK_2_F_BGI-6.txt.gzd0fd8a1bf2ded141ca4f4950ea2adeb6
  NxK_2_R_BGI-6.txt.gzeb949ae2bf5eb06eae1cd91000022227
 80 SRNxK_2_80SR.txt.gz1443538d55b1a36a3cfe579e5403f424
N x K (3)80 PENxK_3_F.txt.gz992d1b2fcfd4d458a9800845987a53ee
  NxK_3_R.txt.gzb29eb33fb7d7eabeb8a4033437063a02
K x N (1)80 PEKxN_1_F.txt.gz13c2aa8bbda896dd89ba9e10728c07f2
  KxN_1_R.txt.gza51ddb07582428b9848636f6897c35bc
K x N (2)80 PEKxN_2_F.txt.gz 639c5f0ba6422a6f024611ca4e27a759
  KxN_2_R.txt.gz ea7259da149b61f72ca6f1a3c04d3a0c
  KxN_2_F_BGI-5.txt.gz45f8dcd3755479868bfcca1b32b675d0
  KxN_2_R_BGI-5.txt.gzf3cbf6e09adf2d4f5f965ea27d172307
  KxN_2_F_BGI-6.txt.gz45fa9cfb80d91b50f5ab48fb95d9b838
  KxN_2_R_BGI-6.txt.gz74d03ffca6a6ca4f7dbd6176e5767bd1
K x N (3)80 SRKxN_3_80SR.txt.gz59ab00827243e0a8838d771d23cc7d00
N x p (1)80 PENxp_1_F.txt.gza21f92c8e78f5a18ed190f2b8cb907c4
  Nxp_1_R.txt.gz9f38f71c05452347459abdfa56b89419
  Nxp_1_F_BGI-5.txt.gze8193b923f0844425715389b7829a9ff
  Nxp_1_R_BGI-5.txt.gzb04b4f70d043c71ed9f3b12ccb9727e7
  Nxp_1_F_BGI-6.txt.gz0a1889bd1e9b143d52bd6e6000bab525
  Nxp_1_R_BGI-6.txt.gze85f110fa04597e9ec37bdc84d8d54f2
N x p (2)80 PENxp_2_F.txt.gze0929bf7e3485b7b3df05b363c1823e1
  Nxp_2_R.txt.gz1a4fe53e1a2756492ab5e4c5bf9a727d
N x p (3)80 PENxp_3_F.txt.gz3994804f53dc0ddefe56794b9d10e556
  Nxp_3_R.txt.gz0a2330f207de7d8dfc6ec3b733189cec
93-11 (1)80 PE93-11_1_F.txt.gz53f2fabeedc6b9910eb47552f8f2651c
  93-11_1_R.txt.gze9f0e120292b838210846413c6ccd002
93-11 (2)80 PE93-11_2_F.txt.gz14b10279bbe5c3e8efd8fadca20facb4
  93-11_2_R.txt.gz02029ad010efdabdcb92b938e0f6063b
  93-11_2_F_BGI-5.txt.gzd9c43c732d4bd983d82a01b80d8b953f
  93-11_2_R_BGI-5.txt.gzc28c054d6302b6513fb23045e2161ea5
  93-11_2_F_BGI-6.txt.gzaa43e3ff1385addc66879cdd30462d37
  93-11_2_R_BGI-6.txt.gz555a4d4b80fae572e23b6022a619ae18
93-11 (3)80 PE93-11_3_F.txt.gzb4937aa8620fa26380a450230f29e82c
  93-11_3_R.txt.gz6c60a864bd9e730df93b78fbecff167e
  93-11_3_F_BGI-5.txt.gz8ddbdb53ec675aa44eb2bb307bf0a8b9
  93-11_3_R_BGI-5.txt.gz3afe14e532220932344c9f463e76e7c4
  93-11_3_F_BGI-6.txt.gz045f961196744cecc169006d71611628
  93-11_3_R_BGI-6.txt.gzbf68d1a782e966a493b844fe93f8aecc
N x 93-11 (1)80 PENx93-11_1_F.txt.gz825382b1e1b097cf9eb880caecd9404f
  Nx93-11_1_R.txt.gzea79768b07c1a5754ba34f60025e21de
  Nx93-11_1_F_BGI-5.txt.gz269974f0093d54186f622bd87a8dab59
  Nx93-11_1_R_BGI-5.txt.gzcb36950e03d900a724750db797fc5572
  Nx93-11_1_F_BGI-6.txt.gze8bf7ba850db325631f8e7ec3da70560
  Nx93-11_1_R_BGI-6.txt.gz4658b98112033097cc937f0b28d5c6c0
N x 93-11 (2)80 PENx93-11_2_F.txt.gzbc9e81e140d3299df5e137880ecddddf
  Nx93-11_2_R.txt.gz47ff85e63543bf96fab933930477b9f7
N x 93-11 (3)80 PENx93-11_3_F.txt.gzdcdd6c74ca8748b7b511cac78d7d9ec9
  Nx93-11_3_R.txt.gz3516c0f7bcdb277fc9af32094e35e5e8
  Nx93-11_3_F_BGI-5.txt.gz90b1b2dcdc849593609f59671b5517f1
  Nx93-11_3_R_BGI-5.txt.gzff5959e7ed942ccb35a527393e92381a
  Nx93-11_3_F_BGI-6.txt.gzb44fd87fd7adae135961adf0484cfe53
  Nx93-11_3_R_BGI-6.txt.gzf526cdab89957de37da416de86201c96
93-11 x N (1)80 PE93-11xN_1_F.txt.gzbeeb64e1df384cfe85533af3ec301966
  93-11xN_1_R.txt.gzb5f69853af71d6914dd61bdc1a7aba45
93-11 x N (2)80 PE93-11xN_2_F.txt.gz4d544f6d95f885e7fe0203189d170097
  93-11xN_2_R.txt.gz550352ac0a7cccd5f455d8bf809ff0c7
  93-11xN_2_F_BGI-5.txt.gzf2a0f40f3e98d965eb8bb0b51bb0f937
  93-11xN_2_R_BGI-5.txt.gz14efee49b01b16931d336fd8372032f8
  93-11xN_2_F_BGI-6.txt.gz876f03b3b712a92b7e2690893756b1a5
  93-11xN_2_R_BGI-6.txt.gzcc1f30c4753aada043b369923369bdff
93-11 x N (3)80 PE93-11xN_3_F.txt.gz9da2b6d373fcd18419060718652d08f0
  93-11xN_3_R.txt.gzb7306ab702333cfd491acbf5652544cc
K x 93-11 (1)80 PEKx93-11_1A_F.txt.gz291eb559354eacb1bd00dbe3888e896c
  Kx93-11_1A_R.txt.gzbb955fe33269a0fdbcc38d6958c8d1c5
  Kx93-11_1B_F.txt.gz7744eed9d364f485d781eecda32eb0d3
  Kx93-11_1B_R.txt.gz2fef7b429f43b62af29abdae4dc9c241
K x 93-11 (2)80 PEKx93-11_2A_F.txt.gzc9f815c3e1944f8bd37c0dc4a9aa7242
  Kx93-11_2A_R.txt.gz20f9a82e19d3dbf9248b535b210ce9da
  Kx93-11_2B_F.txt.gz8eb6be772ab90681d66c43b953fb9066
  Kx93-11_2B_R.txt.gz5bc3d9e0985780fe0ab52cbf0df6aae1
  Kx93-11_2A_F_BGI-5.txt.gz278ebc6b323ef4152ae3166cda05d27a
  Kx93-11_2A_R_BGI-5.txt.gze6f7b04cf847d30a94f30e6f989a4507
  Kx93-11_2A_F_BGI-6.txt.gz583d5697a9866acd36afa5e192bb87d3
  Kx93-11_2A_R_BGI-6.txt.gz86ec1a7980b4f71859f7f511746b1f59
K x 93-11 (3)80 PEKx93-11_3A_F.txt.gzcbde0a56303a168ad810d39dbbe31b3f
  Kx93-11_3A_R.txt.gz59b6bec10105199fd531d5cd680f67d4
  Kx93-11_3B_F.txt.gz39a730f3ec2992916436371075bf707b
  Kx93-11_3B_R.txt.gz4beb95662ca48278c6b660fcf3a3cc02
93-11 x K (1)80 PE99-11xK_1A_F.txt.gz75b53f4cd2bb3139b272d7e59bf9db8e
  99-11xK_1A_R.txt.gzec67326f0cea7ed0bd4e5c3fa903184d
  99-11xK_1B_F.txt.gz4cf280f9d8e1f5c7f75635153acf9867
  99-11xK_1B_R.txt.gza1729f9409e4d3a42ab0720125fc40a9
93-11 x K (2)80 PE93-11xK_2A_F.txt.gzb8b0a9d31f5ee9a8b6af3e04da00b6fa
  93-11xK_2A_R.txt.gz90b8517d40c15e5a17149ec4278d62c8
  93-11xK_2B_F.txt.gzd976e5e3e1d93fe6695e0d20a89c5e02
  93-11xK_2B_R.txt.gzaa038ec37678c9f862683ec5e5f56dc1
93-11 x K (3)80 PE93-11xK_3A_F.txt.gz322579e0dd2d03088839ad7fd40976c0
  93-11xK_3A_R.txt.gz4806316744f914a1a1f97778eb2da2d5
  93-11xK_3B_F.txt.gz42d75ae30520edc617e345f67cbbbc7e
  93-11xK_3B_R.txt.gz57a2473dd55fd01e6ad6dbcbc7a8f4cb
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