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Omics Data

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Bioproject Description Publication GVCF File Library Num.
PRJEB32533 Seed comparative genomics in three coffee species evidence desiccation tolerance mechanisms among intermediate seeds. Stavrinides et al., 2020
9
Library Title Platform Total Base VCF File
ERR3323787 RNA-Seq of Coffea canephora: 3X ploidy ST7 stage plant with seed from Africa, SAMEA5607225, DT1 ILLUMINA 1652783400 bp
ERR3323790 RNA-Seq of Coffea canephora: 3X ploidy ST6 stage plant with seed from Africa, SAMEA5607228, DT4 ILLUMINA 3817512100 bp
ERR3323793 RNA-Seq of Coffea canephora: 3X ploidy ST5 stage plant with seed from Africa, SAMEA5607231, DT7 ILLUMINA 2461312300 bp
ERR3323797 RNA-Seq of Coffea canephora: 3X ploidy ST6 stage plant with seed from Africa, SAMEA5607235, DT11 ILLUMINA 2212856500 bp
ERR3323798 RNA-Seq of Coffea canephora: 3X ploidy ST7 stage plant with seed from Africa, SAMEA5607236, DT12 ILLUMINA 2755226300 bp
ERR3323802 RNA-Seq of Coffea canephora: 3X ploidy ST5 stage plant with seed from Africa, SAMEA5607240, DT16 ILLUMINA 4159006400 bp
ERR3323804 RNA-Seq of Coffea canephora: 3X ploidy ST6 stage plant with seed from Africa, SAMEA5607242, DT18 ILLUMINA 3924157600 bp
ERR3323808 RNA-Seq of Coffea canephora: 3X ploidy ST5 stage plant with seed from Africa, SAMEA5607246, DT22 ILLUMINA 3042409300 bp
ERR3323810 RNA-Seq of Coffea canephora: 3X ploidy ST7 stage plant with seed from Africa, SAMEA5607248, DT24 ILLUMINA 3996371100 bp
PRJNA326055 Raw RNA sequencing data of several cultivated crops and their wild relatives and close outgroups in order to make comparative analyses of the effect of domestication on genome evolution in different crop species. Martin et al., 2020
13
Library Title Platform Total Base VCF File
SRR9203072 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Cote d'Ivoire, C46, CS12 ILLUMINA 2956080400 bp
SRR9203073 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Democratic Republic of the Congo, S19/73, CS13 ILLUMINA 3094132200 bp
SRR9203075 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Kenya, PSE BM 12/8, CB4 ILLUMINA 3403037200 bp
SRR9203078 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Cote d'Ivoire, C41, CS2 ILLUMINA 3016288200 bp
SRR9203079 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Cote d'Ivoire, C47, CS1 ILLUMINA 2984484200 bp
SRR9203080 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Cote d'Ivoire, C55, CS5 ILLUMINA 2676531000 bp
SRR9203081 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Democratic Republic of the Congo, S9/23, CS3 ILLUMINA 3544855800 bp
SRR9203082 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Cote d'Ivoire, C40, CS7 ILLUMINA 3271289200 bp
SRR9203083 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Cote d'Ivoire, D/1/25, CS6 ILLUMINA 3534746000 bp
SRR9203084 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Cote d'Ivoire, Cd235, CS9 ILLUMINA 4597308000 bp
SRR9203085 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Cote d'Ivoire, Cd1, CS8 ILLUMINA 3996281200 bp
SRR9203086 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Cote d'Ivoire, Cd3, CS11 ILLUMINA 2882871000 bp
SRR9203087 RNA-Seq of Coffea canephora: 80 % inflorescence/20 % leaves from Cote d'Ivoire, C27, CS10 ILLUMINA 3302516600 bp
PRJNA353111 This study aimed to identify memory genes of a coffee drought-tolerant clone, it means, genes that respond to multiple drought exposures. Lemos et al., 2020
12
Library Title Platform Total Base VCF File
SRR5074356 RNA-Seq of Coffea canephora: 9 months one drought cycle treatment plant with leaves from Brazil: Espirito Santo, Clone 109 ILLUMINA 12914390000 bp
SRR5074358 RNA-Seq of Coffea canephora: 9 months one drought cycle treatment plant with leaves from Brazil: Espirito Santo, Clone 120 ILLUMINA 9507315000 bp
SRR5074359 RNA-Seq of Coffea canephora: 9 months watered (control) treatment plant with leaves from Brazil: Espirito Santo, Clone 109 ILLUMINA 10035755200 bp
SRR5074360 RNA-Seq of Coffea canephora: 9 months watered (control) treatment plant with leaves from Brazil: Espirito Santo, Clone 120 ILLUMINA 10386512400 bp
SRR5074361 RNA-Seq of Coffea canephora: 9 months watered (control) treatment plant with leaves from Brazil: Espirito Santo, Clone 120 ILLUMINA 13988906200 bp
SRR5074362 RNA-Seq of Coffea canephora: 9 months one drought cycle treatment plant with leaves from Brazil: Espirito Santo, Clone 120 ILLUMINA 10802253800 bp
SRR5074363 RNA-Seq of Coffea canephora: 9 months three drought cycles treatment plant with leaves from Brazil: Espirito Santo, Clone 120 ILLUMINA 9833940600 bp
SRR5074365 RNA-Seq of Coffea canephora: 9 months watered (control) treatment plant with leaves from Brazil: Espirito Santo, Clone 120 ILLUMINA 10282667000 bp
SRR5074366 RNA-Seq of Coffea canephora: 9 months three drought cycles treatment plant with leaves from Brazil: Espirito Santo, Clone 109 ILLUMINA 12330143400 bp
SRR5074368 RNA-Seq of Coffea canephora: 9 months three drought cycles treatment plant with leaves from Brazil: Espirito Santo, Clone 120 ILLUMINA 10857576000 bp
SRR5074370 RNA-Seq of Coffea canephora: 9 months one drought cycle treatment plant with leaves from Brazil: Espirito Santo, Clone 120 ILLUMINA 10516221000 bp
SRR5074371 RNA-Seq of Coffea canephora: 9 months three drought cycles treatment plant with leaves from Brazil: Espirito Santo, Clone 120 ILLUMINA 10070530800 bp
PRJNA529218 Transcriptome analysis of ARF and Aux/IAA expression during the induction of somatic embryogenesis in Coffea canephora. Méndez-Hernández et al., 2021
12
Library Title Platform Total Base VCF File
SRR8787530 RNA-Seq of Coffea canephora: 14 days DBI MS salts without growth regulators pre-embryogenic condition plant with leaves, GSM3688000 ILLUMINA 4608966100 bp
SRR8787531 RNA-Seq of Coffea canephora: 14 days DBI MS salts without growth regulators pre-embryogenic condition plant with leaves, GSM3688001 ILLUMINA 3375831744 bp
SRR8787532 RNA-Seq of Coffea canephora: 9 days DBI MS salts with naphthaleneacetic acid (ANA) and kinetin (KIN) pre-embryogenic condition plant with leaves, GSM3688002 ILLUMINA 3275678678 bp
SRR8787533 RNA-Seq of Coffea canephora: 9 days DBI MS salts with naphthaleneacetic acid (ANA) and kinetin (KIN) pre-embryogenic condition plant with leaves, GSM3688003 ILLUMINA 3290224719 bp
SRR8787534 RNA-Seq of Coffea canephora: 0 days DBI MS salts with naphthaleneacetic acid (ANA) and kinetin (KIN) pre-embryogenic condition plant with leaves, GSM3688004 ILLUMINA 4125183092 bp
SRR8787535 RNA-Seq of Coffea canephora: 0 days DBI MS salts with naphthaleneacetic acid (ANA) and kinetin (KIN) pre-embryogenic condition plant with leaves, GSM3688005 ILLUMINA 3699471270 bp
SRR8787536 RNA-Seq of Coffea canephora: 1 day DAI Yasuda salts with benzyladenine (BA) embryogenic condition plant with leaves, GSM3688006 ILLUMINA 2869417463 bp
SRR8787537 RNA-Seq of Coffea canephora: 1 day DAI Yasuda salts with benzyladenine (BA) embryogenic condition plant with leaves, GSM3688007 ILLUMINA 3583173961 bp
SRR8787538 RNA-Seq of Coffea canephora: 2 days DAI Yasuda salts with benzyladenine (BA) embryogenic condition plant with leaves, GSM3688008 ILLUMINA 6527614374 bp
SRR8787539 RNA-Seq of Coffea canephora: 2 days DAI Yasuda salts with benzyladenine (BA) embryogenic condition plant with leaves, GSM3688009 ILLUMINA 4677860268 bp
SRR8787540 RNA-Seq of Coffea canephora: 21 days DAI Yasuda salts with benzyladenine (BA) embryogenic condition plant with leaves, GSM3688010 ILLUMINA 4262165713 bp
SRR8787541 RNA-Seq of Coffea canephora: 21 days DAI Yasuda salts with benzyladenine (BA) embryogenic condition plant with leaves, GSM3688011 ILLUMINA 3887878055 bp
PRJNA561881 Global analysis of gene activity and valuable genes during Coffea canephora coffee bean development. Dong et al., 2019
12
Library Title Platform Total Base VCF File
SRR10019307 RNA-Seq of Coffea canephora: small green fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF1_1 BGISEQ 7002128800 bp
SRR10019308 RNA-Seq of Coffea canephora: red fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF4_1 BGISEQ 6977465200 bp
SRR10019309 RNA-Seq of Coffea canephora: yellow fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF3_3 BGISEQ 6530829000 bp
SRR10019310 RNA-Seq of Coffea canephora: yellow fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF3_2 BGISEQ 6752324600 bp
SRR10019311 RNA-Seq of Coffea canephora: yellow fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF3_1 BGISEQ 6763097200 bp
SRR10019312 RNA-Seq of Coffea canephora: large green fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF2_3 BGISEQ 6801165200 bp
SRR10019313 RNA-Seq of Coffea canephora: large green fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF2_2 BGISEQ 6790616600 bp
SRR10019314 RNA-Seq of Coffea canephora: large green fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF2_1 BGISEQ 6546807800 bp
SRR10019315 RNA-Seq of Coffea canephora: small green fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF1_3 BGISEQ 6977841000 bp
SRR10019316 RNA-Seq of Coffea canephora: red fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF4_3 BGISEQ 7007907800 bp
SRR10019317 RNA-Seq of Coffea canephora: red fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF4_2 BGISEQ 6995011600 bp
SRR10019318 RNA-Seq of Coffea canephora: small green fruit stage coffee bean from China:RuiLi\, Yunnan, Robusta, CcF1_2 BGISEQ 7007529400 bp
PRJNA729673 A systems approach to understand the impact of climate changes in Coffea spp. Fernandes et al., 2021
9
Library Title Platform Total Base VCF File
SRR14522110 RNA-Seq of Coffea canephora: severe water deficit treatment plant with leaves from Portugal, cv. Conilon, 3_3C_25_380_SWD, 3_3C ILLUMINA 4441593574 bp
SRR14522111 RNA-Seq of Coffea canephora: severe water deficit treatment plant with leaves from Portugal, cv. Conilon, 3_3B_25_380_SWD, 3_3B ILLUMINA 5155691248 bp
SRR14522112 RNA-Seq of Coffea canephora: severe water deficit treatment plant with leaves from Portugal, cv. Conilon, 3_3A_25_380_SWD, 3_3A ILLUMINA 4432765770 bp
SRR14522113 RNA-Seq of Coffea canephora: mild water deficit treatment plant with leaves from Portugal, cv. Conilon, 2_2C_25_380_MWD, 2_2C ILLUMINA 8740860372 bp
SRR14522114 RNA-Seq of Coffea canephora: mild water deficit treatment plant with leaves from Portugal, cv. Conilon, 2_2B_25_380_MWD, 2_2B ILLUMINA 5868196152 bp
SRR14522115 RNA-Seq of Coffea canephora: mild water deficit treatment plant with leaves from Portugal, cv. Conilon, 2_2A_25_380_MWD, 2_2A ILLUMINA 3841964654 bp
SRR14522116 RNA-Seq of Coffea canephora: well-watered treatment plant with leaves from Portugal, cv. Conilon, 1_1C_25_380_WW, 1_1C ILLUMINA 4787557358 bp
SRR14522125 RNA-Seq of Coffea canephora: well-watered treatment plant with leaves from Portugal, cv. Conilon, 1_1B_25_380_WW, 1_1B ILLUMINA 4017015632 bp
SRR14522126 RNA-Seq of Coffea canephora: well-watered treatment plant with leaves from Portugal, cv. Conilon, 1_1A_25_380_WW, 1_1A ILLUMINA 4310239640 bp
PRJNA787748 A systems approach to understand the impact of climate changes in Coffea spp. Marques et al., 2023
18
Library Title Platform Total Base VCF File
SRR17191235 RNA-Seq of Coffea canephora: well-watered-elevated CO2 treatment plant with leaves from Portugal, Conilon, 4_4A, 4 ILLUMINA 4496900366 bp
SRR17191236 RNA-Seq of Coffea canephora: severe water deficit-ambient CO2 treatment plant with leaves from Portugal, Conilon, 3_3C, 3 ILLUMINA 4441593574 bp
SRR17191237 RNA-Seq of Coffea canephora: severe water deficit-ambient CO2 treatment plant with leaves from Portugal, Conilon, 3_3B, 3 ILLUMINA 5155691248 bp
SRR17191238 RNA-Seq of Coffea canephora: severe water deficit-ambient CO2 treatment plant with leaves from Portugal, Conilon, 3_3A, 3 ILLUMINA 4432765770 bp
SRR17191239 RNA-Seq of Coffea canephora: mild water deficit-ambient CO2 treatment plant with leaves from Portugal, Conilon, 2_2C, 2 ILLUMINA 8740860372 bp
SRR17191240 RNA-Seq of Coffea canephora: mild water deficit-ambient CO2 treatment plant with leaves from Portugal, Conilon, 2_2B, 2 ILLUMINA 5868196152 bp
SRR17191247 RNA-Seq of Coffea canephora: mild water deficit-ambient CO2 treatment plant with leaves from Portugal, Conilon, 2_2A, 2 ILLUMINA 3841964654 bp
SRR17191258 RNA-Seq of Coffea canephora: well-watered-ambient CO2 treatment plant with leaves from Portugal, Conilon, 1_1C, 1 ILLUMINA 4787557358 bp
SRR17191261 RNA-Seq of Coffea canephora: severe water deficit-elevated CO2 treatment plant with leaves from Portugal, Conilon, 6_6C, 6 ILLUMINA 4325191478 bp
SRR17191262 RNA-Seq of Coffea canephora: severe water deficit-elevated CO2 treatment plant with leaves from Portugal, Conilon, 6_6B, 6 ILLUMINA 3308318428 bp
SRR17191263 RNA-Seq of Coffea canephora: severe water deficit-elevated CO2 treatment plant with leaves from Portugal, Conilon, 6_6A, 6 ILLUMINA 4004661312 bp
SRR17191264 RNA-Seq of Coffea canephora: mild water deficit-elevated CO2 treatment plant with leaves from Portugal, Conilon, 5_5D, 5 ILLUMINA 5577204244 bp
SRR17191265 RNA-Seq of Coffea canephora: mild water deficit-elevated CO2 treatment plant with leaves from Portugal, Conilon, 5_5B, 5 ILLUMINA 5572729944 bp
SRR17191266 RNA-Seq of Coffea canephora: mild water deficit-elevated CO2 treatment plant with leaves from Portugal, Conilon, 5_5A, 5 ILLUMINA 4100369720 bp
SRR17191267 RNA-Seq of Coffea canephora: well-watered-elevated CO2 treatment plant with leaves from Portugal, Conilon, 4_4C, 4 ILLUMINA 4499342344 bp
SRR17191268 RNA-Seq of Coffea canephora: well-watered-elevated CO2 treatment plant with leaves from Portugal, Conilon, 4_4B, 4 ILLUMINA 4218395492 bp
SRR17191269 RNA-Seq of Coffea canephora: well-watered-ambient CO2 treatment plant with leaves from Portugal, Conilon, 1_1B, 1 ILLUMINA 4017015632 bp
SRR17191270 RNA-Seq of Coffea canephora: well-watered-ambient CO2 treatment plant with leaves from Portugal, Conilon, 1_1A, 1 ILLUMINA 4310239640 bp
PRJNA798825 The raw sequencing data of Coffea canephora and Camellia sinensis Tang et al., 2022
18
Library Title Platform Total Base VCF File
SRR17673022 RNA-Seq of Coffea canephora: 10 years plant with leaf from China, Qunti, L52 ILLUMINA 3298781188 bp
SRR17673023 RNA-Seq of Coffea canephora: 10 years plant with leaf from China, Qunti, L51 ILLUMINA 3290331672 bp
SRR17673024 RNA-Seq of Coffea canephora: 10 years plant with leaf from China, Qunti, L42 ILLUMINA 3245024706 bp
SRR17673025 RNA-Seq of Coffea canephora: 10 years plant with leaf from China, Qunti, L41 ILLUMINA 3238397008 bp
SRR17673026 RNA-Seq of Coffea canephora: 10 years plant with leaf from China, Qunti, L32 ILLUMINA 3393178588 bp
SRR17673027 RNA-Seq of Coffea canephora: 10 years plant with leaf from China, Qunti, L31 ILLUMINA 3385937838 bp
SRR17673028 RNA-Seq of Coffea canephora: 10 years plant with leaf from China, Qunti, L22 ILLUMINA 2985461138 bp
SRR17673029 RNA-Seq of Coffea canephora: 10 years plant with leaf from China, Qunti, L21 ILLUMINA 2977735604 bp
SRR17673030 RNA-Seq of Coffea canephora: 10 years plant with stem from China, Qunti, S42 ILLUMINA 3381244534 bp
SRR17673031 RNA-Seq of Coffea canephora: 10 years plant with stem from China, Qunti, S41 ILLUMINA 3373342492 bp
SRR17673032 RNA-Seq of Coffea canephora: 10 years plant with stem from China, Qunti, S32 ILLUMINA 3304156114 bp
SRR17673033 RNA-Seq of Coffea canephora: 10 years plant with stem from China, Qunti, S31 ILLUMINA 3296227530 bp
SRR17673034 RNA-Seq of Coffea canephora: 10 years plant with stem from China, Qunti, S22 ILLUMINA 3356223680 bp
SRR17673035 RNA-Seq of Coffea canephora: 10 years plant with stem from China, Qunti, S21 ILLUMINA 3346724554 bp
SRR17673036 RNA-Seq of Coffea canephora: 10 years plant with stem from China, Qunti, S12 ILLUMINA 3338961714 bp
SRR17673037 RNA-Seq of Coffea canephora: 10 years plant with stem from China, Qunti, S11 ILLUMINA 3331046626 bp
SRR17673038 RNA-Seq of Coffea canephora: 10 years plant with leaf from China, Qunti, L12 ILLUMINA 3365521820 bp
SRR17673039 RNA-Seq of Coffea canephora: 10 years plant with leaf from China, Qunti, L11 ILLUMINA 3362519984 bp

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