####### NOTES ############################################################################################### ## The Trichomes sequences files were supplied to SGN by Dr. M. Larson in sff format. ## fasta and qual files were extracted using sff_extract script () ## These files are equivalent to SRR files in the SRA database: ## (SRR015436, SRR015435, SRR027943, SRR027942, SRR027941, SRR027940, SRR027939 ## were downloaded from SRA database (http://www.ncbi.nlm.nih.gov/sites/entrez search in SRA database for ## 'Solanum lycopersicum' 03-Feb-2010). ############################################################################################################## ###### EQUIVALENCES ########################################################################################## ## Trichomes_LA0716_Spe454.fasta AND Trichomes_LA0716_Spe454.fasta.qual = SRR027939 ## Trichomes_LA1589_Spi454.fasta AND Trichomes_LA1589_Spi454.fasta.qual = SRR027942 ## Trichomes_LA1708_Sar454.fasta AND Trichomes_LA1708_Sar454.fasta.qual = SRR027943 ## Total_Trichomes_LA1777_Sha454.fasta AND Total_Trichomes_LA1777_Sha454.fasta.qual = SRR027940 ## TypeVI_Trichomes_LA1777_Sha454.fasta AND TypeVI_Trichomes_LA1777_Sha454.fasta.qual = SRR027941 ## Total_Trichomes_LA3475_Sly454.fasta AND Total_Trichomes_LA3475_Sly454.fasta.qual = SRR015435 ## TypeVI_Trichomes_LA3475_Sly454.fasta AND TypeVI_Trichomes_LA3475.fasta.qual = SRR015436 ############################################################################################################## ##### GENBANK INFORMATION #################################################################################### SGN_FILENAME: TypeVI_Trichomes_LA3475_Sly454.fasta and TypeVI_Trichomes_LA3475_Sly454.fasta.qual GENBANK_ACCESSION: SRR015436 STUDY: Transcriptome analysis of Solanum lycopersicum trichomes Design: Total RNA was extracted from type VI trichomes isolated from stem and petiole tissues of 3-week-old Solanum lycopersicum cv M82 plants and used directly for cDNA synthesis using the Clontech SMART cDNA synthesis kit with slight modification to kit protocols. Reverse transcription of RNA was performed using a modified primer with sequence: 5'-TAGAGACCGAGGCGGCCGACATGTTTTGTTTTTTTTTCTTTTTTTTTTVN-3'. After PCR amplication, cDNA was purified using the Qiagen QIAquick PCR purification kit. 5ug of cDNA was submitted for sequencing by the Michigan State University sequencing facility according to the standard Roche 454 GS-FLX protocol. PLATFORM: LS454 LIBRARY NAME: LA3475 Type VI LIBRARY SPECIE: Solanum lycopersicum LIBRARY STRATEGY: EST LIBRARY SOURCE: NON GENOMIC LIBRARY SELECTION: RANDOM LIBRARY LAYOUT: SINGLE LIBRARY CONSTRUCTION PROTOCOL: Standard 454 library construction protocol NUMBER OF SPOTS: 336745 // SGN_FILENAME: Total_Trichomes_LA3475_Sly454.fasta and Total_Trichomes_LA3475_Sly454.fasta.qual GENBANK_ACCESSION: SRR015435 STUDY: Total RNA was extracted from total trichomes isolated from stem and petiole tissues of 3-week-old Solanum lycopersicum cv M82 plants and used directly for cDNA synthesis using the Clontech SMART cDNA synthesis kit according to kit protocols. 5ug of size selected SfiI digested cDNA was submitted for sequencing by the Michigan State University sequencing facility according to the standard Roche 454 GS-20 protocol. PLATFORM: LS454 LIBRARY NAME: LA3475 LIBRARY SPECIE: Solanum lycopersicum LIBRARY STRATEGY: EST LIBRARY SOURCE: NON GENOMIC LIBRARY SELECTION: RANDOM LIBRARY LAYOUT: SINGLE LIBRARY CONSTRUCTION PROTOCOL: Standard 454 library construction protocol NUMBER OF SPOTS: 361911 // SGN_FILENAME: Trichomes_LA1708_Sar454.fasta and Trichomes_LA1708_Sar454.fasta.qual GENBANK_ACCESSION: SRR027943 STUDY: Total RNA was extracted from enriched fractions of type VI trichomes isolated from stem tissue of Solanum arcanum LA1708 plants and used directly for cDNA synthesis using the Clontech SMART cDNA synthesis kit according to kit protocols but with modified primers. Size selected SfiI digested cDNA was submitted for sequencing by the Michigan State University sequencing facility according to the standard Roche 454 GS-FLX protocol. Primers used in the construction of this library: RT1: 5%u2019-TAGAGGCCGAGGCGGCCGACATGTTTTGTTTTTTTTTCTTTTTTTTTTVN-3%u2019; RT2: 5%u2019 %u2013CGCAAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGG-3%u2019; 5%u2019PCR primer: 5%u2019-AAGCAGTGGTATCAACGCAGAGT-3%u2019; 3%u2019PCR primer: 5%u2019-TAGAGGCCGAGGCGGCCGAC-3%u2019 PLATFORM: LS454 LIBRARY NAME: LA1708 LIBRARY SPECIE: Solanum arcanum LIBRARY STRATEGY: EST LIBRARY SOURCE: NON GENOMIC LIBRARY SELECTION: RANDOM LIBRARY LAYOUT: SINGLE LIBRARY CONSTRUCTION PROTOCOL: Standard 454 library construction protocol NUMBER OF SPOTS: 495068 // SGN_FILENAME: Trichomes_LA1589_Spi454.fasta and Trichomes_LA1589_Spi454.fasta.qual GENBANK_ACCESSION: SRR027942 STUDY: Total RNA was extracted from enriched fractions of type VI trichomes isolated from leaf tissue of Solanum pimpinellifolium LA1589 plants and used directly for cDNA synthesis using the Clontech SMART cDNA synthesis kit according to kit protocols but with modified primers. Size selected SfiI digested cDNA was submitted for sequencing by the Michigan State University sequencing facility according to the standard Roche 454 GS-FLX protocol. Primers used in the construction of this library: RT1: 5%u2019-TAGAGGCCGAGGCGGCCGACATGTTTTGTTTTTTTTTCTTTTTTTTTTVN-3%u2019; RT2: 5%u2019 %u2013CGCAAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGG-3%u2019; 5%u2019PCR primer: 5%u2019-AAGCAGTGGTATCAACGCAGAGT-3%u2019; 3%u2019PCR primer: 5%u2019-TAGAGGCCGAGGCGGCCGAC-3%u2019 PLATFORM: LS454 LIBRARY NAME: LA1589 LIBRARY SPECIE: Solanum pimpinellifollium LIBRARY STRATEGY: EST LIBRARY SOURCE: NON GENOMIC LIBRARY SELECTION: RANDOM LIBRARY LAYOUT: SINGLE LIBRARY CONSTRUCTION PROTOCOL: Standard 454 library construction protocol NUMBER OF SPOTS: 299847 // SGN_FILENAME: Type_VI_Trichomes_LA1777_Sha454.fasta and Type_VI_Trichomes_LA1777_Sha454.fasta.qual GENBANK_ACCESSION: SRR027941 STUDY: Total RNA was extracted from enriched fractions of type VI trichomes isolated from leaf tissue of Solanum habrochaites LA1777 plants and used directly for cDNA synthesis using the Clontech SMART cDNA synthesis kit according to kit protocols but with modified primers. Size selected SfiI digested cDNA was submitted for sequencing by the Michigan State University sequencing facility according to the standard Roche 454 GS-FLX protocol. Primers used in the construction of this library: RT1: 5%u2019-TAGAGGCCGAGGCGGCCGACATGTTTTGTTTTTTTTTCTTTTTTTTTTVN-3%u2019; RT2: 5%u2019 %u2013CGCAAGCAGTGGTATCAACGCAGAGTGGCCATTACGGCCGGG-3%u2019; 5%u2019PCR primer: 5%u2019-AAGCAGTGGTATCAACGCAGAGT-3%u2019; 3%u2019PCR primer: 5%u2019-TAGAGGCCGAGGCGGCCGAC-3%u2019 PLATFORM: LS454 LIBRARY NAME: LA1777 LIBRARY SPECIE: Solanum habrochaites LIBRARY STRATEGY: EST LIBRARY SOURCE: NON GENOMIC LIBRARY SELECTION: RANDOM LIBRARY LAYOUT: SINGLE LIBRARY CONSTRUCTION PROTOCOL: Standard 454 library construction protocol NUMBER OF SPOTS: 329070 // SGN_FILENAME: Total_Trichomes_LA1777_Sha454.fasta and Total_Trichomes_LA1777_Sha454.fasta.qual GENBANK_ACCESSION: SRR027940 STUDY: Total RNA was extracted from total trichomes isolated from leaf tissue of Solanum habrochaites LA1777 plants and used directly for cDNA synthesis using the Clontech SMART cDNA synthesis kit according to kit protocols with some modifications. After amplification of cDNA, size selection and removal of primers was performed using the Qiagen QIAquick PCR purification kit. cDNA was submitted for sequencing by the Michigan State University sequencing facility according to the standard Roche 454 GS-FLX protocol. PLATFORM: LS454 LIBRARY NAME: LA1777 LIBRARY SPECIE: Solanum habrochaites LIBRARY STRATEGY: EST LIBRARY SOURCE: NON GENOMIC LIBRARY SELECTION: RANDOM LIBRARY LAYOUT: SINGLE LIBRARY CONSTRUCTION PROTOCOL: Standard 454 library construction protocol NUMBER OF SPOTS: 132402 // SGN_FILENAME: Trichomes_LA0716_Spe454.fasta and Trichomes_LA0716_Spe454.fasta.qual GENBANK_ACCESSION: SRR027939 STUDY: Total RNA was extracted from total trichomes isolated from leaf tissue of Solanum pennellii LA0716 plants and used directly for cDNA synthesis using the Clontech SMART cDNA synthesis kit with slight modification to kit protocols. Reverse transcription of RNA was performed using a modified primer with sequence: 5'-TAGAGGCCGAGGCGGCCGACATGTTTTGTTTTTTTTTCTTTTTTTTTTVN-3'. Size selected SfiI digested cDNA was submitted for sequencing by the Michigan State University sequencing facility according to the standard Roche 454 GS-FLX protocol. PLATFORM: LS454 LIBRARY NAME: LA0716 LIBRARY SPECIE: Solanum pennellii LIBRARY STRATEGY: EST LIBRARY SOURCE: NON GENOMIC LIBRARY SELECTION: RANDOM LIBRARY LAYOUT: SINGLE LIBRARY CONSTRUCTION PROTOCOL: Standard 454 library construction protocol NUMBER OF SPOTS: 344190 //