"# A complete submission will include a completed template (this page), processed data files, and raw data files. " # Most fields in this template must be completed. Incomplete submissions will not be processed. # Templates containing example data are found in the METADATA EXAMPLE 1 and 2 spreadsheet tabs at the foot of this page. # Field names (in blue) should not be edited. Hover over cells containing field names to view field content guidelines. SERIES # This section describes the overall experiment. title Transcriptome sequencing of Pacific oyster Crassostrea gigas summary Deep sequencing of mRNA from Pacific oyster Crassostrea gigas overall design "Analysis of ploy(A)+ RNA of different specimens:8 organs,38 developmental stages and 61 experimental processed organs from Pacific oyster Crassostrea gigas" contributor Xiaodong Fang contributor Li Li SRA_center_name_code [optional] SAMPLES "# This section lists and describes each of the biological Samples under investgation, as well as any protocols that are specific to individual Samples" "# If multiple processed or raw data files exist per Sample, they can either be referenced in separate columns as shown in the METADATA EXAMPLE 1 spreadsheet or referenced on separate rows, as shown in the METADATA EXAMPLE 2 spreadsheet." Sample name title source name organism characteristics: developmental stage characteristics: Colony characteristics: tag molecule description raw file raw file type raw file MD5 checksum barcode Man1 Man1 outer edge of mantle Crassostrea gigas adult total RNA "Sequenced reads were generated from outer edge of mantle in Crassostrea gigas, this part of tissue is along the edge of shells and is thought to be rich of sensory elements, as well as responsible for the extension of shell." Man1_1.fq.gz fastq d7e1e9109bd71e334af7047a3965c2ab Man1_2.fq.gz fastq 99acc345a2433f2e872373b3083efaaa Dgl Dgl digestive gland Crassostrea gigas adult total RNA "Sequenced reads were generated from digestive gland in Crassostrea gigas, the sample includes all the tissues in visceral mass." Dgl_1.fq.gz fastq 4d1d3674876aa2b42ffcd616aece2a97 Dgl_2.fq.gz fastq 2a6efaea12b205e317a7ae4dfcc00809 Fgo Fgo female gonad Crassostrea gigas adult total RNA "Sequenced reads were generated from female gonad in Crassostrea gigas. The individual whose organs are isolated and sampled respectively is a female.The gonad is full of eggs as oyster has millions of eggs in the gland at mature season, while the gland tissue maybe only take up very few part." Fgo_1.fq.gz fastq 77f65bd1ff06d31eb3ddb4e421d3e9e9 Fgo_2.fq.gz fastq 8bf52179d48f0d435a1331ed002cc75c Gil Gil gill Crassostrea gigas adult total RNA Sequenced reads were generated from gill in Crassostrea gigas. Gil_1.fq.gz fastq 419066be9b3c2637fb407ebabd6c1414 Gil_2.fq.gz fastq 9d797188420ec7c6f617c8477c7331d0 Man2 Man2 inner part of mantle Crassostrea gigas adult total RNA Sequenced reads were generated from the inner part of mantle in Crassostrea gigas. The inner part of mantle and the inner surface of shell are in close proximity. Man2_1.fq.gz fastq d1c8498b2fec6def189d205af4d05741 Man2_2.fq.gz fastq 9a03634dd53ad1f5b362bc2bc95ebba8 Amu Amu adductor muscle Crassostrea gigas adult total RNA Sequenced reads were generated from adductor muscle in Crassostrea gigas. Amu_1.fq.gz fastq accd50c5a50afb051c7556cde91d34e4 Amu_2.fq.gz fastq 6c41f9fb224b9bcd42b812b7e77ece88 Hem Hem hemolymph Crassostrea gigas adult total RNA Sequenced reads were generated from hemolymph in Crassostrea gigas. The RNA were extracted from the blood. Hem_1.fq.gz fastq 1ffd57dcc2bf73383fdf52e6500eff20 Hem_2.fq.gz fastq a3f6aa98b4ccc096c424eea723e1053c Lpa Lpa labial palp Crassostrea gigas adult total RNA "Sequenced reads were generated from labial palp in Crassostrea gigas, an organ just out of the mouth." Lpa_1.fq.gz fastq 227d2c85dac759825d7294a8ec47dc4f Lpa_2.fq.gz fastq a50a35fcfa9dd32ba68b2d01df865258 Mgo Mgo male gonad Crassostrea gigas adult total RNA "Sequenced reads were generated from male gonad in Crassostrea gigas. The male gonad is sampled from a individual in the F1 generation of the ""G3"" family." Mgo_1.fq.gz fastq 6afc276dbd477117b2234daa415df20d Mgo_2.fq.gz fastq 6e7d80908a1d9d91c1fc7b411fdc64b1 Rem Rem remainder Crassostrea gigas adult total RNA "Sequenced reads were generated from the mixture of remainder tissues in Crassostrea gigas after sampling the main part of hemolymph, mantle, gonad, digestive gland, gill, labial palp, and adductor muscle." Rem_1.fq.gz fastq 10a86d89693995710f5436c2177dad2a Rem_2.fq.gz fastq 1e1364ec320ad13367252a6e0de8ca84 early early early developmental stages Crassostrea gigas adult total RNA "Sequenced reads were generated from early developmental stages in Crassostrea gigas. The early developmetnal stages including the stage of second polar body ejected at 35 min after insemination, four cells stage at 1.5 h, morula stage at 3.5 h, the stage when embryo can rotate at 5.5 h, early gastrula stage at 7.5 h, early trochophore stage at 9.5 h, trochophore at 11.5 h, trochophore at 13.5 h, early D-shaped larvae at 15.5 h, D-shaped larvae at 17.5 h, and D-shaped larvae at 19.5 h." early_1.fq.gz fastq 8e9c6e32e47ce71be37c72452ad1e56e early_2.fq.gz fastq 6748d374ee0becf367b2ad0cdf04629d late late late planktonic stages and spat Crassostrea gigas adult total RNA "Sequenced reads were generated from late planktonic stages and spat in Crassostrea gigas, including the stage of D-shaped larvae at 21.5 h, D-shaped larvae at 1.75 day, D-shaped larvae at 3.77 day, early umbo larvae at 5.73 day, umbo larvae at 7.75 day, umbo larvae at 9.75 day, umbo larvae at 11.75 day, umbo larvae at 13.75 day, umbo larvae at 15.75 day, eyed larvae at 16.75 day, and spat at 22.15 day." late_1.fq.gz fastq 2f6cd6bb4057b05d03d250dc2d106fac late_2.fq.gz fastq 59176538e7bae0a7829f94ffa2659d4c G3 G3 G3 Crassostrea gigas adult total RNA "Sequenced reads were generated from the female gonad of an individual of ""G3"" family in Crassostrea gigas." G3_1.fq.gz fastq b274a8e7c5ce2fe06861984981141e37 G3_2.fq.gz fastq 256fd566dd2bb6aa910ebfbd26d43016 E E egg Crassostrea gigas egg total RNA Sequenced reads were generated from the egg stage at 0 h in Crassostrea gigas. E.fq.gz fastq ede63fde36f0ba49fec34043c93f1372 TC TC two cells Crassostrea gigas two cells total RNA Sequenced reads were generated from the stage of two cell at 1 h 20 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. TC.fq.gz fastq 7426985c7a9615c3d9d3072331f72f91 FC FC four cells Crassostrea gigas four cells total RNA Sequenced reads were generated from the stage of four cell at 1 h 32 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. FC.fq.gz fastq b012cbe7b2b79a3d0b605a50dd101bd8 EM EM early morula stage Crassostrea gigas early morula stage total RNA Sequenced reads were generated from the stage of early morula at 2 h 25 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. EM.fq.gz fastq cac281fc264bd9642e2bb777789f2433 M M morula stage Crassostrea gigas morula stage total RNA Sequenced reads were generated from the stage of morula at 3 h 30 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. M.fq.gz fastq e7fb748fbd89c074029bd494ce75d26e B B blastula stage Crassostrea gigas blastula stage total RNA Sequenced reads were generated from the stage of blatula at 4 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. B.fq.gz fastq 298fa922e03d30d9d03eb25578a56b82 RM RM rotary movement Crassostrea gigas rotary movement total RNA Sequenced reads were generated from the stage when the embryo start rotate at 5 h 30 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. RM.fq.gz fastq fd1bf88fa73abbfa8ba489a1361be5c6 FS FS free swimming Crassostrea gigas free swimming total RNA Sequenced reads were generated from the stage when the embryo can freely swimming at 6 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. FS.fq.gz fastq 9c8a4267b3103896ac7f2eb4cb9bcb1e EG EG early gastrula stage Crassostrea gigas early gastrula stage total RNA Sequenced reads were generated from the stage of early gastrula at 7 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. EG.fq.gz fastq 375cde97e9b5ff289328573315e81fdb G G gastrula stage Crassostrea gigas gastrula stage total RNA Sequenced reads were generated from the stage of gastrula at 8 h 30 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. G.fq.gz fastq 7a50b2f33bee11932b7e4b3d8915792f T1 T1 trochophore1 Crassostrea gigas trochophore1 total RNA Sequenced reads were generated from the stage of trochophore at 9 h 30 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. T1.fq.gz fastq 57f668a781a6f76bcb729a219ddcae08 T2 T2 trochophore2 Crassostrea gigas trochophore2 total RNA Sequenced reads were generated from the stage of trochophore at 11 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. T2.fq.gz fastq c96135b4696ea2e293c6638f71a3337e T3 T3 trochophore3 Crassostrea gigas trochophore3 total RNA Sequenced reads were generated from the stage of trochophore at 12 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. T3.fq.gz fastq 034459b7c34565f4509e4e00a8869ff5 T4 T4 trochophore4 Crassostrea gigas trochophore4 total RNA Sequenced reads were generated from the stage of trochophore at 13 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. T4.fq.gz fastq 1604c60fbd6cb45c4175330fee32188c T5 T5 trochophore5 Crassostrea gigas trochophore5 total RNA Sequenced reads were generated from the stage of trochophore at 14 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. T5.fq.gz fastq c8886ec6a14fc73374409bf8b598de1b ED1 ED1 early Dshaped larva1 Crassostrea gigas early Dshaped larva1 total RNA Sequenced reads were generated from the stage of early D-shaped larvae at 15 h 30 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. ED1.fq.gz fastq d58a0c3f2e53f90bc54d7c91462ed02b ED2 ED2 early Dshaped larva2 Crassostrea gigas early Dshaped larva2 total RNA Sequenced reads were generated from the stage of early D-shaped larvae at 16 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. ED2.fq.gz fastq d09811e1b1f5e6b7a4b0fd3eaac131f9 D1 D1 Dshaped larva1 Crassostrea gigas Dshaped larva1 total RNA Sequenced reads were generated from the stage of D-shaped larvae at 17 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. D1.fq.gz fastq 2bbfee33a7a622d2471eafc44c950dad D2 D2 Dshaped larva2 Crassostrea gigas Dshaped larva2 total RNA Sequenced reads were generated from the stage of D-shaped larvae at 18 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. D2.fq.gz fastq 6ec4e1fb7f4de5907125aca465fe0612 D3 D3 Dshaped larva3 Crassostrea gigas Dshaped larva3 total RNA Sequenced reads were generated from the stage of D-shaped larvae at 19 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. D3.fq.gz fastq 3cde21629d59bb2913fa7eb33a100ff1 D4 D4 Dshaped larva4 Crassostrea gigas Dshaped larva4 total RNA Sequenced reads were generated from the stage of D-shaped larvae at 20 h 35 min after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. D4.fq.gz fastq 9caa61ecca4cb09405d57aec305f8b4f D5 D5 Dshaped larva5 Crassostrea gigas Dshaped larva5 total RNA Sequenced reads were generated from the stage of D-shaped larvae at 1.09 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. D5.fq.gz fastq 87ece38f2e0cafb435c9d6b9189a74f2 D6 D6 Dshaped larva6 Crassostrea gigas Dshaped larva6 total RNA Sequenced reads were generated from the stage of D-shaped larvae at 1.75 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. D6.fq.gz fastq da9f37cb8e8a6359f1e68d91d2e3a38c D7 D7 Dshaped larva7 Crassostrea gigas Dshaped larva7 total RNA Sequenced reads were generated from the stage of D-shaped larvae at 3.77 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt. D7.fq.gz fastq 814daad554b508964b813d40006ac718 EU1 EU1 early umbo larva1 Crassostrea gigas early umbo larva1 total RNA Sequenced reads were generated from the stage of early umbo larvae at 4.77 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. EU1.fq.gz fastq 79090b981652c9e5591af560bfc67829 EU2 EU2 early umbo larva2 Crassostrea gigas early umbo larva2 total RNA Sequenced reads were generated from the stage of early umbo larvae at 6.75 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. EU2.fq.gz fastq 2fbeb3d41d7c630d351eb84ccb4af7db U1 U1 umbo larva1 Crassostrea gigas umbo larva1 total RNA Sequenced reads were generated from the stage of umbo larvae at 7.75 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. U1.fq.gz fastq 0cc1cf14fd89fcddfd4fedc4b0018930 U2 U2 umbo larva2 Crassostrea gigas umbo larva2 total RNA Sequenced reads were generated from the stage of umbo larvae at 8.75 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. U2.fq.gz fastq a9da92cc1f41edde8263cd6fccdc7786 U3 U3 umbo larva3 Crassostrea gigas umbo larva3 total RNA Sequenced reads were generated from the stage of umbo larvae at 9.75 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. U3.fq.gz fastq b0b9ebdc1f2ec5368f8f0df1156ae654 U4 U4 umbo larva4 Crassostrea gigas umbo larva4 total RNA Sequenced reads were generated from the stage of umbo larvae at 10.77 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. U4.fq.gz fastq 1255a365ad7d167871c1795394e2c8af U5 U5 umbo larva5 Crassostrea gigas umbo larva5 total RNA Sequenced reads were generated from the stage of umbo larvae at 12.76 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. U5.fq.gz fastq d15ba4a0a6c9e2f7128505e4e5bcce16 U6 U6 umbo larva6 Crassostrea gigas umbo larva6 total RNA Sequenced reads were generated from the stage of umbo larvae at 13.75 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. U6.fq.gz fastq 30f4e79df8502ecde30503a1f58ffab1 LU1 LU1 later umbo larva1 Crassostrea gigas later umbo larva1 total RNA Sequenced reads were generated from the stage of late umbo larvae at 14.73 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. LU1.fq.gz fastq 3de564bbd8f393f6e1abd6010688890b LU2 LU2 later umbo larva2 Crassostrea gigas later umbo larva2 total RNA Sequenced reads were generated from the stage of late umbo larvae at 15.73 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. LU2.fq.gz fastq 882eef648277762751ca1e6c616f44d7 P1 P1 competent pediveliger for metamorphosis Crassostrea gigas competent pediveliger for metamorphosis total RNA Sequenced reads were generated from the stage of eyed larvae at 18.03 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. P1.fq.gz fastq f886d9eb6395c9728c485f62e2323289 P2 P2 competent pediveliger for metamorphosis Crassostrea gigas competent pediveliger for metamorphosis total RNA Sequenced reads were generated from the stage of eyed larvae at 18.19 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. P2.fq.gz fastq eb12f4fa17ac4be372820b1b43d65c29 S S spat Crassostrea gigas spat total RNA Sequenced reads were generated from the stage of spat at 22.15 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of 30 ppt before the 4.77 day. The temperature became 25 ºC from the 4.77 day. S.fq.gz fastq 9f507fe088a6ad48002983bd943d4e37 J J juvenile Crassostrea gigas juvenile total RNA Sequenced reads were generated from the stage of juvenile at 215 day after insemination in Crassostrea gigas. The culture was performed in seawater with the temperature of 26 ºC and the salinity of before the 4.77 day. The temperature became 25 ºC from the 4.77 day to the first one month. Then the culutre was performed in natural sea area. J.fq.gz fastq 8d25763ffaf113a36d5876d9ed37774b temperature_5 temperature_5 "Pool of three oyster gills, sampled at time 7d, 5 ºC " Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 5 ºC for 7 days." temperature_5.fq.gz fastq cc8899aa1fd51f57085c3285b3adf594 temperature_10 temperature_10 "Pool of three oyster gills, sampled at time 7d, 10 ºC" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 10 ºC for 7 days." temperature_10.fq.gz fastq 9fff3e4cf126b5f45b65e9d8d2cec8a2 temperature_15 temperature_15 "Pool of three oyster gills, sampled at time 7d, 15 ºC" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 15 ºC for 7 days." temperature_15.fq.gz fastq 681ee69a5f05eac09107e87458040289 temperature_20 temperature_20 "Pool of three oyster gills, sampled at time 7d, 20 ºC" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 20 ºC for 7 days." temperature_20.fq.gz fastq 278ce5c92d6e72c77273bf675aacad0c temperature_25 temperature_25 "Pool of three oyster gills, sampled at time 7d, 25 ºC" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 25 ºC for 7 days." temperature_25.fq.gz fastq a1c88f9ff84b2e604dd2146f53ec74ea temperature_30 temperature_30 "Pool of three oyster gills, sampled at time 12h, 30 ºC" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 30 ºC for 12 hours." temperature_30.fq.gz fastq 3743cebd52d73df68f904ad0c13576f1 temperature_35 temperature_35 "Pool of three oyster gills, sampled at time 12h, 35 ºC" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with 35 ºC for 12 hours." temperature_35.fq.gz fastq 5e8798cf38ec04bfb8257024a880a112 salt_5 salt_5 "Pool of three oyster gills, sampled at time 12h, salinity 5 ppt" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 5 ppt for 7 days." salt_5.fq.gz fastq 63d0f5837c38355ecef64c938781a7b7 salt_10 salt_10 "Pool of three oyster gills, sampled at time 12h, salinity 10 ppt" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 10 ppt for 7 days." salt_10.fq.gz fastq 6bd2dcdbf7f72525231471e59c922c58 salt_15 salt_15 "Pool of three oyster gills, sampled at time 12h, salinity 15 ppt" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 15 ppt for 7 days." salt_15.fq.gz fastq 2966acb6cc40a9eef2ef3230688186df salt_20 salt_20 "Pool of three oyster gills, sampled at time 12h, salinity 20 ppt" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 20 ppt for 7 days." salt_20.fq.gz fastq 4f1c24b28d08a3ceb645c1726dafb3c3 salt_25 salt_25 "Pool of three oyster gills, sampled at time 12h, salinity 25 ppt" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 25 ppt for 7 days." salt_25.fq.gz fastq 0915b3c5cea9653ea1be73f1566b881c salt_30 salt_30 "Pool of three oyster gills, sampled at time 12h, salinity 30 ppt" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 30 ppt for 7 days." salt_30.fq.gz fastq b8b12a02c26d6637d4115b0cf741a820 salt_40 salt_40 "Pool of three oyster gills, sampled at time 12h, salinity 40 ppt" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with salinity 40 ppt for 7 days." salt_40.fq.gz fastq 3ca329e2007b12a13ff2825801b950c1 dried_gills_1d dried_gills_1d "Pool of three oyster gills, sampled at time 1d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 1 days. During the whole expriment, the oyster were under starvation. " dried_gills_1d.fq.gz fastq a7efc4b5592c41ec23732c10c4aee4ea dried_gills_3d dried_gills_3d "Pool of three oyster gills, sampled at time 3d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 3 days. During the whole expriment, the oyster were under starvation." dried_gills_3d.fq.gz fastq 40122430c1c72eebf7f0f98fa813f378 dried_gills_5d dried_gills_5d "Pool of three oyster gills, sampled at time 5d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 5 days. During the whole expriment, the oyster were under starvation." dried_gills_5d.fq.gz fastq 0c76464554b2c790c90d482181cccec8 dried_gills_7d dried_gills_7d "Pool of three oyster gills, sampled at time 7d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 7 days. During the whole expriment, the oyster were under starvation." dried_gills_7d.fq.gz fastq 67af913ba2eafcbc11edad25d2406ca0 dried_gills_9d dried_gills_9d "Pool of three oyster gills, sampled at time 9d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 9 days. During the whole expriment, the oyster were under starvation." dried_gills_9d.fq.gz fastq 06ee7a256dcddd16adaab20f89fa0f34 dried_gills_10d dried_gills_10d "Pool of three oyster gills, sampled at time 10d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 10 days. During the whole expriment, the oyster were under starvation." dried_gills_10d.fq.gz fastq 4561004df0e377bfc1e18fd1920be2fe dried_gills_11d dried_gills_11d "Pool of three oyster gills, sampled at time 11d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with exposure to air for 11 days. During the whole expriment, the oyster were under starvation." dried_gills_11d.fq.gz fastq 57c32a7c0c6d2e3fb1e6025d51db7570 dried_muscle_0d dried_muscle_0d "Pool of three oyster adductor muscles, sampled at time 0d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster adductor muscles, samples was collected immidiately after the treatment." dried_muscle_0d.fq.gz fastq 4b216cda351007600cd963a6ad6fbf38 dried_muscle_1d dried_muscle_1d "Pool of three oyster adductor muscles, sampled at time 1d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 1 days. During the whole expriment, the oyster were under starvation." dried_muscle_1d.fq.gz fastq de3618a9804f7555a9d6c0e0339a7195 dried_muscle_3d dried_muscle_3d "Pool of three oyster adductor muscles, sampled at time 3d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 3 days. During the whole expriment, the oyster were under starvation." dried_muscle_3d.fq.gz fastq 3bde2c9a9762b19b835ed27e4a4eca28 dried_muscle_5d dried_muscle_5d "Pool of three oyster adductor muscles, sampled at time 5d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 5 days. During the whole expriment, the oyster were under starvation." dried_muscle_5d.fq.gz fastq aa5d5b6fb8f2a387891208160fbbb2ba dried_muscle_7d dried_muscle_7d "Pool of three oyster adductor muscles, sampled at time 7d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 7 days. During the whole expriment, the oyster were under starvation." dried_muscle_7d.fq.gz fastq 7be74c95c7602d4e88ef4af0f4d5be1e dried_muscle_9d dried_muscle_9d "Pool of three oyster adductor muscles, sampled at time 9d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 9 days. During the whole expriment, the oyster were under starvation." dried_muscle_9d.fq.gz fastq 8045261ab554c7c8063174f01fe7ce43 dried_muscle_10d dried_muscle_10d "Pool of three oyster adductor muscles, sampled at time 10d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 10 days. During the whole expriment, the oyster were under starvation." dried_muscle_10d.fq.gz fastq e8196e18c2f22ee10a03e15993cb5bcf dried_muscle_11d dried_muscle_11d "Pool of three oyster adductor muscles, sampled at time 11d, exposure to air" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster adductor muscles, which were treated with exposure to air for 11 days. During the whole expriment, the oyster were under starvation." dried_muscle_11d.fq.gz fastq 209a04f9c020d7652ad34640946ed214 Zn12h_gills Zn12h_gills "Pool of three oyster gills, sampled at time 12h, Zn" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (1 mg/L) for 12 hours. " Zn12h_gills.fq.gz fastq 477443a62be9e3f95982378280b6dfaf Pb12h_gills Pb12h_gills "Pool of three oyster gills, sampled at time 12h, Pb" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Plumbum (500 ug/L) for 12 hours." Pb12h_gills.fq.gz fastq 628d8b20655ece6c8e216213f94ce772 Cu12h_gills Cu12h_gills "Pool of three oyster gills, sampled at time 12h, Cu" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Copper (100 ug/L) for 12 hours." Cu12h_gills.fq.gz fastq 516260885e0c7c79eff128f2bf61af18 Hg12h_gills Hg12h_gills "Pool of three oyster gills, sampled at time 12h, Hg" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Hydrargyrum (100 ug/L) for 12 hours." Hg12h_gills.fq.gz fastq 7034434412ea9d83d96230c4d846a3cf Cd12h_gills Cd12h_gills "Pool of three oyster gills, sampled at time 12h, Cd" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Cadmium(100 ug/L) for 12 hours." Cd12h_gills.fq.gz fastq d5d84e2c0ede3ff20d8ba57e7af5f4b0 Zn_Cd12h_gills Zn_Cd12h_gills "Pool of three oyster gills, sampled at time 12h, Zn & Cd" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (500 _g/L) and Cadmium (50 _g/L) for 12 hours." Zn_Cd12h_gills.fq.gz fastq fa6286e4458940907803e1c150beb9c2 Pb12h_DG Pb12h_DG "Pool of three oyster digestive glands, sampled at time 12h, Pb" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Plumbum (500 ug/L) for 12 hours." Pb12h_DG.fq.gz fastq 4fb3b0d0ec578a7d948fec1f6637e9b8 Cu12h_DG Cu12h_DG "Pool of three oyster digestive glands, sampled at time 12h, Cu" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Copper (100 ug/L) for 12 hours." Cu12h_DG.fq.gz fastq b39ca7ef1c3be7c776e2885258014ae0 Hg12h_DG Hg12h_DG "Pool of three oyster digestive glands, sampled at time 12h, Hg" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Hydrargyrum (100 ug/L) for 12 hours." Hg12h_DG.fq.gz fastq fe1ab60b435b89a33ce222423ef9b22c Cd12h_DG Cd12h_DG "Pool of three oyster digestive glands, sampled at time 12h, Cd" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Cadmium(100 ug/L) for 12 hours." Cd12h_DG.fq.gz fastq 33a6135fbba57d772c9e05b8d843b498 Zn_Cd12h_DG Zn_Cd12h_DG "Pool of three oyster digestive glands, sampled at time 12h, Zn & Cd" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (500 _g/L) and Cadmium (50 _g/L) for 12 hours." Zn_Cd12h_DG.fq.gz fastq 4a386193ef10ffd7e729c6acc4826675 Pb9d_gills Pb9d_gills "Pool of three oyster gills, sampled at time 9d, Pb" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Plumbum (500 ug/L) for 9 days." Pb9d_gills.fq.gz fastq 5571222ec7931212901b0639db18dbef Cu9d_gills Cu9d_gills "Pool of three oyster gills, sampled at time 9d, Cu" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Copper (100 ug/L) for 9 days." Cu9d_gills.fq.gz fastq 57ffc24b93772cc88d36384a431e8b88 Hg9d_gills Hg9d_gills "Pool of three oyster gills, sampled at time 9d, Hg" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Hydrargyrum (100 ug/L) for 9 days." Hg9d_gills.fq.gz fastq da9ec4f124d54908390fd43566e081c6 Pb9d_DG Pb9d_DG "Pool of three oyster digestive glands, sampled at time 9d, Pb" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Plumbum (500 ug/L) for 9 days." Pb9d_DG.fq.gz fastq 945b639e4abef63bbf993a4f25824c0a Cu9d_DG Cu9d_DG "Pool of three oyster digestive glands, sampled at time 9d, Cu" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Copper (100 ug/L) for 9 days." Cu9d_DG.fq.gz fastq fe68563a8893d87b829a1766768fda57 Hg9d_DG Hg9d_DG "Pool of three oyster digestive glands, sampled at time 9d, Hg" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Hydrargyrum (100 ug/L) for 9 days." Hg9d_DG.fq.gz fastq 1e73868cefe3eeb6c1ab4b51139af559 Cd9d_gills Cd9d_gills "Pool of three oyster gills, sampled at time 9d, Cd" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Cadmium(100 ug/L) for 9 days." Cd9d_gills.fq.gz fastq a354ce52293c288163b30ba199581556 Zn_Cd9d_gills Zn_Cd9d_gills "Pool of three oyster gills, sampled at time 9d, Zn & Cd" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (500 _g/L) and Cadmium (50 _g/L) for 9 days." Zn_Cd9d_gills.fq.gz fastq 35ea0b05d0365a8207b3edf9d3770dcc Cd9d_DG Cd9d_DG "Pool of three oyster digestive glands, sampled at time 9d, Cd" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Cadmium(100 ug/L) for 9 days." Cd9d_DG.fq.gz fastq 34f0c372371d5cf9e89ccb2632c70cff Zn_Cd9d_DG Zn_Cd9d_DG "Pool of three oyster digestive glands, sampled at time 9d, Zn & Cd" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (500 _g/L) and Cadmium (50 _g/L) for 9 days." Zn_Cd9d_DG.fq.gz fastq 9415121ed816d927f97664de678eb51d Metal_C-gills Metal_C-gills "Pool of three oyster gills, with no metals challenge" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were with no metals challenges." Metal_C-gills.fq.gz fastq ab161c29e00ab266ec7ffc9222b4ef5f Metal_C-DG Metal_C-DG "Pool of three oyster digestive glands, with no metals challenge" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were with no metals challenges." Metal_C-DG.fq.gz fastq d21cd4672634e1eeb03a29d403943587 Zn12h_DG Zn12h_DG "Pool of three oyster digestive glands, sampled at time 12h, Zn" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (1 mg/L) for 12 hours. " Zn12h_DG.fq.gz fastq 0ff9df5f1c3717553adbca1c322d977f Zn5d_DG Zn5d_DG "Pool of three oyster digestive glands, sampled at time 5d, Zn" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (1 mg/L) for 5 days. " Zn5d_DG.fq.gz fastq be0af0ca190911c020b19b31b73c69fb Zn7d_DG Zn7d_DG "Pool of three oyster digestive glands, sampled at time 7d, Zn" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (1 mg/L) for 7 days. " Zn7d_DG.fq.gz fastq 248f611a49643b15fae92ae0afdcb201 Zn9d_DG Zn9d_DG "Pool of three oyster digestive glands, sampled at time 9d, Zn" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (1 mg/L) for 9 days. " Zn9d_DG.fq.gz fastq 6dfaf0408639aec6ca8c9e5c76fea565 Zn13d_DG Zn13d_DG "Pool of three oyster digestive glands, sampled at time 13d, Zn" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster digestive glands, which were treated with Zinc (1 mg/L) for 13 days. " Zn13d_DG.fq.gz fastq 3823f7bf37d6331be892753bc9886eb3 Zn5d_gills Zn5d_gills "Pool of three oyster digestive gills, sampled at time 5d, Zn" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (1 mg/L) for 5 days. " Zn5d_gills.fq.gz fastq 17848acb278ed3868f111ae92dc27533 Zn7d_gills Zn7d_gills "Pool of three oyster digestive gills, sampled at time 7d, Zn" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (1 mg/L) for 7 days. " Zn7d_gills.fq.gz fastq 0f0f7f6a97e116cb3ac40ffd6200581a Zn9d_gills Zn9d_gills "Pool of three oyster digestive gills, sampled at time 9d, Zn" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (1 mg/L) for 9 days. " Zn9d_gills.fq.gz fastq b61145ae856c819d38a03fb61e25138d Zn13d_gills Zn13d_gills "Pool of three oyster digestive gills, sampled at time 13d, Zn" Crassostrea gigas adult total RNA "Sequenced reads were generated from the pool of three adult oyster gills, which were treated with Zinc (1 mg/L) for 13 days. " Zn13d_gills.fq.gz fastq 6f276f3ae076636d7dfd38a28e3ed5e8 PROTOCOLS # This section includes protocols and fields which are common to all Samples. # Any protocols which are applicable to specific Samples should be included as additional columns of the SAMPLES section instead. growth protocol treatment protocol total RNA is extracted by TRIzol Reagent library construction protocol "For RNA-seq, poly-A+ RNA was isolated with 30 oligo-dT-coupled beads from 20 _g total RNA of each sample. First strand cDNA synthesis was performed with random hexamers and Superscript II reverse transcriptase (Invitrogen). The second strand was synthesized with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. After end repair and addition of a 3’ dA overhang the cDNA was ligated to Illumina PE adapter oligo mix, and size selected to 200±20 bp fragments by gel purification. After 15 cycles of PCR amplification the libraries were sequenced using a 1G Illumina Genome Analyzer and the paired-end sequencing module." library strategy RNA-seq library source genomic library selection cDNA instrument model Illumina HiSeq 2000 data processing "use Pacific oyster Crassostrea gigas genome as reference, sequenced reads were aligned onto the corresponding reference using TopHat v1.0.12 with default parameters except -r 20 --mate-std-dev 5 -g 20 -I 10000 --solexa1.3-quals" IMPORTANT NOTES Barcode/Multiplexed Data "At this time, we prefer that submitters split run files so that each barcoded sample ends up with a dedicated run file based on the barcode sequences. If this is not possible, please provide the barcode sequences, adapter/linker sequences and any additional information necessary to interpret the raw data files." Paired-End Data Please also provide average insert size (fragment length) and standard deviation of the paired-end libraries. You can include this information in the library construction protocol field. Raw Data Files "*** Raw data files should contain the original, primary analysis (unprocessed) output***. Base calls and quality scores are required. Please generate one fastq files per lane." Acceptable Raw Data File Types: Please see http://www.ncbi.nlm.nih.gov/geo/info/seq.html for complete instructions. qseq.txt files Native files generated by the primary analysis program Bustard in Illumina pipeline versions 1.3 and later. It is important to package these files in the form: .tar.gz _seq.txt and _prb.txt files Native files generated by the primary analysis program Bustard in Illumina pipeline versions 1.3 and earlier. It is important to package these files in the form: .tar.gz SRF files "For Illumina pipeline versions 1.1 and 1.3, the conduit for primary data is the sequence read format (SRF). " Fastq files "Fastq files should contain all the original data, i.e., the reads should be complete (not trimmed subsequences), and unfiltered (e.g., it is not sufficient to submit only sequences that align). Please generate one fastq file per lane. " # Other text formats "Illumina pipeline 1.4 outputs raw data in other text formats as well. These should be OK provided that the files contain all the original data, i.e., the reads should be complete (not trimmed subsequences), unfiltered (e.g., it is not sufficient to submit only sequences that align)."