mRNA-Seq data from Solanum prinophyllum meristems

Zach Lippman's lab in CSHL prodcued the mRNA-Seq data of S. prinophyllum in this directory. Five distinct developmental stages (two biological replicates of each) of S. prinophyllum shoot apical meristems were collected for mRNA samples: Middle Vegetative Meristem (MVM), Transition Meristem (TM), Floral Meristem (FM), Sympodial Inflorescence Meristem (SIM), and SYmpodial shoot Meristem (SYM). Illumina paired-end 100bp sequencing libraries were made following standard Illumina library preparation protocols, and sequenced on a HiSeq 2000 with four samples in a lane. The raw fastq files of the reads were provided labeled with Library ID number and barcode ("R1" and "R2" indicate read pairs). 

In total, 517,475,030 (X 2) reads were generated. A de novo assembly of these reads was conducted by Zachary Lemmon in CSHL using Trinity (trinityrnaseq_r20140717, --trimmomatic --normalize_reads). In total, 189,729 contigs were obtained, of which 79,340 were longer than 1,000 bp. The assembly has a size of 231,356,151 bp and N50 of 2,116 bp. The assembly was provided with the file 'sprino_denovo_20140814.fa' in the directory. 

Additional information are available from lippman@cshl.edu

LID291444	ACAGTG	S. prinophyllum	MVM1
LID291445	GCCAAT	S. prinophyllum	TM1
LID291446	CTTGTA	S. prinophyllum	SIM1
LID291447	CAGATC	S. prinophyllum	FM1
LID291448	CGATGT	S. prinophyllum	SYM1
LID291449	TGACCA	S. prinophyllum	MVM2
LID291450	ACAGTG	S. prinophyllum	TM2
LID291451	CTTGTG	S. prinophyllum	FM2
LID292993	GCCAAT	S. prinophyllum	SIM2
LID292994	CAGATC	S. prinophyllum	SYM2