ERX1604042 E-MTAB-4855:Sample 1_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250328 SAMEA4079218 Sample 1_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: optimal temperature growth condition Experimental Factor: LA17777 cultivar ERX1604043 E-MTAB-4855:Sample 10_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250329 SAMEA4079219 Sample 10_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: cold temperature growth condition Experimental Factor: cv. Moneymaker cultivar ERX1604044 E-MTAB-4855:Sample 11_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250330 SAMEA4079220 Sample 11_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: cold temperature growth condition Experimental Factor: cv. Moneymaker cultivar ERX1604045 E-MTAB-4855:Sample 12_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250331 SAMEA4079221 Sample 12_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: cold temperature growth condition Experimental Factor: cv. Moneymaker cultivar ERX1604046 E-MTAB-4855:Sample 2_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250332 SAMEA4079222 Sample 2_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: optimal temperature growth condition Experimental Factor: LA17777 cultivar ERX1604047 E-MTAB-4855:Sample 3_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250333 SAMEA4079223 Sample 3_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: optimal temperature growth condition Experimental Factor: LA1777 cultivar ERX1604048 E-MTAB-4855:Sample 4_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250334 SAMEA4079224 Sample 4_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: optimal temperature growth condition Experimental Factor: cv. Moneymaker cultivar ERX1604049 E-MTAB-4855:Sample 5_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250335 SAMEA4079225 Sample 5_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: optimal temperature growth condition Experimental Factor: cv. Moneymaker cultivar ERX1604050 E-MTAB-4855:Sample 6_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250336 SAMEA4079226 Sample 6_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: optimal temperature growth condition Experimental Factor: cv. Moneymaker cultivar ERX1604051 E-MTAB-4855:Sample 7_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250337 SAMEA4079227 Sample 7_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: cold temperature growth condition Experimental Factor: LA1777 cultivar ERX1604052 E-MTAB-4855:Sample 8_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250338 SAMEA4079228 Sample 8_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: cold temperature growth condition Experimental Factor: LA1777 cultivar ERX1604053 E-MTAB-4855:Sample 9_p ERP016476 Root transcriptome profiling in chilling-sensitive tomato (S. lycopersicum cv. Moneymaker) and the more cold-tolerant wild tomato S. habrochaites LA1777 compared at optimal and suboptimal temperature. ERS1250339 SAMEA4079229 Sample 9_p RNA-Seq TRANSCRIPTOMIC cDNA Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Seeds of S. lycopersicum cv. Moneymaker and S. habrochaites LA1777 were germinated in a climate-controlled room at 23°C as described above. Five-day-old germinated seedlings were separated into two groups: half of them were transferred to an identical climate room at 15°C (suboptimal-temperature treatment), whereas the other half remained in the room at 23°C (near-optimal temperature treatment). After 3 days, three replicates of whole roots were collected from both genotypes at the two temperature treatments and immediately frozen in liquid nitrogen. The samples were stored at −80°C until RNA extraction. Total RNA from whole roots was extracted by TRIzol reagent according to the manufacturer’s instructions (Sigma-Aldrich). The quantity and quality of total RNA treated with RNase-free DNase I (Thermo Scientific) were determined by an Agilent Technologies 2100 Bioanalyzer and RNA samples with RNA integrity number (RIN) > 8 were used for the RNA sequencing and quantitative RT-PCR analysis. Illumina HiSeq2500 (with v4 kit) and Nextera XT sample preparation kits were used for RNA sequencing and all raw reads were paired-end sequenced. Reads for each of the 12 samples were processed by CLC genomics workbench and were aligned to ITAG-cDNA 2.1 (with S. lycopersicum as reference genome). Read counts of each sample were used to quantify the gene expression. Differential expression analysis was carried out with the negative binomial test of DESeq R package v1.20.0 (Anders and Huber, 2010). The False Discovery Rate (FDR) threshold according the multiple testing correction of Benjamini–Hochberg FDR method (Benjamini and Hochberg, 1995) was applied and genes with an adjusted P-value (Padj ≤ 0.05) and log2-fold change in the ratio between 15 and 23°C of more than 1 and less than -1 defined the significantly differentially expressed genes (DEGs). The Plant MetGenMAP system was used to identify significantly altered pathways and for gene ontology (GO) term enrichment analysis (Joung et al, 2009). Functional annotation was retrieved from Panther (http://pantherdb.org) and SGN tomato (http://solgenomics.net). 252 0 F Application Read Forward 1 1 R Application Read Reverse 127 Illumina HiSeq 2500 Experimental Factor: cold temperature growth condition Experimental Factor: LA1777 cultivar