Readme Document describing raw sequence read files and assembled transcriptome for Nematostella Vectensis early embryonic development.

to be published in: "A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a model for de novo assembly in emerging model systems" by Sarah Tulin, Derek Aguiar, Sorin Istrail and Joel Smith

Nematostella Embryonic Transcriptome

created from Illumina HiSeq 100bp paired end reads.  

cDNA libraries and raw reads created by Sarah Tulin, for questions contant: stulin@mbl.edu
transcriptome assembly performed by Derek Aguiar, for questionas contact: rap@cs.brown.edu

Transcriptome File
The assembled transcriptome is in "Trinity.fasta", 85MB

The transcriptome was assembled using all reads from all timepoints filtered for quality. Adapter contaminants and rRNA contaminants were also removed.  The remaining reads were assembled de novo using the Trinity Assembler, release 2011-08-20

Raw Read Files
The raw reads are grouped by timepoint (0hours, 6hours, 12hours, 18hours, 24Ahours, 24Bhours)

24AHour and 24BHour are biological replicates from separate animal spawning events.

The 6-letter code in the file name is the index used

L002 indicates all reads came from a single lane, lane 2 in this case

R1 and R2 correspond to Read 1 and Read 2 for paired end reads and the last number 001-010 is the file number.

The files are zipped fastq files that can be unzipped, quality controlled filtered and assembled using Trinity, Velvet and Oases, Trans-ABySS or another assembler.