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Revision as of 16:57, 25 March 2013

Rice CHIP-Seq Sequence Files

  • 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
K4 9 (1) 50SE K4_9_1.fq.gz c13977bcaa08eb480fba5e7b84e36897
50SE K4_9_1-2.fq.gz c815a48f833336bc8cb1d8a573c02c6f
9 (2) 50SE K4_9_2.fq.gz 03483d0192bb2275c2e0a77ddb0dfcf8
K (1) 50SE K4_K_1.fq.gz 54cb7cd94870f807c9efaf3f802e38fb
50SE K4_K_1-2.fq.gz a987b452061f4f285e3616998c0c9c69
K (2) 50SE K4_K_2.fq.gz 0b7ece83d0236c60353f95b177d49d6d
N (1) 50SE K4_N_1.fq.gz b1afc052057d2b5e0e4c04109de6f0fe
N (2) 50SE K4_N_2.fq.gz 5559b063c22a4ce4976abe22e972826c
50SE K4_N_2-2.fq.gz 8da79cae0a68a3c5c0dfd59d94de3d12
p (1) 50SE K4_p_1.fq.gz 4fa8b78c46b6e86d11ab1c7c5afbabe6
p (2) 50SE K4_p_2.fq.gz 3c2c87792b631ecdff291abb73b4de99
50SE K4_p_2-2.fq.gz 5d4c1a851d48be0b06e33dd5f0ea3fb6
9K (1) 50SE K4_9K_1.fq.gz f271c08d599b7a163ea5b9105dfd95bb
50SE K4_9K_1-2.fq.gz 485c20c5bb8d546b9a64fbe3c2dd3c80
9K (2) 50SE K4_9K_2.fq.gz 9b44d69bf87c763170cd7a08f1a7ba96
K9 (1) 50SE K4_K9_1.fq.gz fa8915f3d8d4171c35dbf06b28f194fb
K9 (2) 50SE K4_K9_2.fq.gz 2b425999f1dd828ddbfdd647e86e9037
50SE K4_K9_2-2.fq.gz 8ca5fd11e3783a620d76ca52e0ac9c85
9N (1) 50SE K4_9N_1.fq.gz 3ccba6ae27de53695403c25268998936
50SE K4_9N_1-2.fq.gz 5a749a327a6900268eacfa81dcc74ab0
9N (2) 50SE K4_9N_2.fq.gz 4925634bfc37bae027d029618120e0a9
50SE K4_9N_2-2.fq.gz 2cf32d9c70ec30361444eccc117c7d58
N9 (1) 50SE K4_N9_1.fq.gz d49de8bb0cb7758fbb92a52dd4de9598
50SE K4_N9_1-2.fq.gz 190f85cfa3151478e032e8ed4282aa1b
N9 (2) 50SE K4_N9_2.fq.gz e91bdbc90af4813c0e2c8d4963b5460a
50SE K4_N9_2-2.fq.gz 067926b149a6daab76b8d7995773f706
50SE K4_N9_2-3.fq.gz d3285b8d93ffc8311a22c2cb0dd2731d
KN (1) 50SE K4_KN_1.fq.gz 8d9bbcbbe1b5d49ba2a8f3d3618b132d
50SE K4_KN_1-2.fq.gz 8cdf2d4624a868c0f1059a5436b2bd86
KN (2) 50SE K4_KN_2.fq.gz 846475bb0cbca31e28bd4d5b61eda15f
50SE K4_KN_2-2.fq.gz 6ca901535f9608090e19da894fff203f
NK (1) 50SE K4_NK_1.fq.gz e211974225a44e9590f8f74748fad57d
50SE K4_NK_1-2.fq.gz 7e7cfa29e170ab1a801ec95f7e4f7a4f
NK (2) 50SE K4_NK_2.fq.gz 1b1fbca37866bc467109e9472628b812
50SE K4_NK_2-2.fq.gz 5bcf9471658ee8b03dbc67dec9d16677
K27 9 (1) 50SE K27_9_1a.fq.gz 538aa048518f45e3042e292853fa096c
50SE K27_9_1a-2.fq.gz 9bc944617db31ac11756d9ab9dd9460a
50SE K27_9_1b.fq.gz 88b9564cc32cd999bee75dacf5958096
9 (2) 50SE K27_9_2a.fq.gz f83cc98f29e08447bb4e9bafd70998a9
50SE K27_9_2a-2.fq.gz e7c48298dc5f76ca3ef4cef61ce308b1
50SE K27_9_2b.fq.gz 6579e209e1487a5a3c98b7f292a47abf
50SE K27_9_2b-2.fq.gz e03837e610e635ebbce7d4db39d02c5a
Input * 9 (1) 50SE Input_9_1.fq.gz bb47bc63d04eac9acafb3921173eb974
9 (2) 50SE Input_9_2.fq.gz c25387ad0968f564f5a40ddd21722ea4
K (1) 50SE Input_K_1.fq.gz 522ef13424c895496bf572d8827037ac
K (2) 50SE Input_K_2.fq.gz f98cc11193c571c1300446026bcc30c0
N (1) 50SE Input_N_1.fq.gz 4271dd7223f9f8e014d965203fd8b0e5
N (2) 50SE Input_N_2.fq.gz 0d7530dbb8515555b7758e09dc8380b2
p (1) 50SE Input_p_1.fq.gz cc5298cf473ddc3cd71ef3c97ce4c5d6
p (2) 50SE Input_p_2.fq.gz 5808291d9e4e800f6f2030395ff3a4ac
9K (1) 50SE Input_9K_1.fq.gz 305c78564cdbf1208fd08c502eeb82bf
9K (2) 50SE Input_9K_2.fq.gz 5f73e33e7888c47a7ea4ba851db71e22
K9 (1) 50SE Input_K9_1.fq.gz b5926e5ae75425765d3c8ff97ed24ad9
K9 (2) 50SE Input_K9_2.fq.gz 036e5a68d1ee4b506179a4d6872c1519
9N (1) 50SE Input_9N_1.fq.gz fcfb3e3b81f4d63ef2b52b9201ddc8b1
9N (2) 50SE Input_9N_2.fq.gz 9e3167a0a1edce55c0b09b3b0660437a
N9 (1) 50SE Input_N9_1.fq.gz b650258c8a0f8031bba8337a47de77b2
N9 (2) 50SE Input_N9_2.fq.gz f04733215ad233154bc746c4b0994a0d
KN (1) 50SE Input_KN_1.fq.gz 2b6a21d99ffd8907e9402993ea46ad58
KN (2) 50SE Input_KN_2.fq.gz cbd04cb5d8bbf428765632e67023dd7f
NK (1) 50SE Input_NK_1.fq.gz 35313a89463775b9ff545c4d0a93a1e5
NK (2) 50SE Input_NK_2.fq.gz a4f979078f2cd68ee8940413a13e4bba
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