Macrobrachium rosenbergii developmental transcriptomes - SRA

SRX189206: Macrobrachium rosenbergii developmental transcriptomes
1 ILLUMINA (Illumina HiSeq 2000) run: 592 spots, 116,100 bases, 206,280b downloads

Design: Total RNA from 200 M. rosenbergii larvae (Zoea 4 to 11) and PL2-28 was isolated. Equal amounts of RNA were pooled into four pools, each containing RNA from 40-60 individuals of 5 larval or PL sub-stages (8-15 individuals at each sub-stage), in duplicate. To ensure representation of low abundance transcripts in the transcriptome assembly, each of the four pools was divided into two tubes of which one was subjected to enzymatic normalization. All eight samples were used for the de novo assembly, while differential expression was calculated only for the four non-normalized pools. These eight total samples were subjected to next generation sequencing by Fasteris Life Science (Geneva, Switzerland) on an Illumina Genome Analyzer (HighSeq 2000, Illumina, San Diego, CA), performing 100 bp–paired end sequencing on one lane. The sequence reads were separated into the 8 libraries according to their indexes (de-multiplexing) and stored as FASTQ files. This yielded a total of ~242 million reads, with 14-38 (average 30) million reads per library. To create a reference transcriptome, all reads were de novo assembled using Velvet, with several K-mer values, followed by Oases. The pair-read insert average size was set at 200 bases, with a standard deviation of 10%.

Submitted by: BEN-GURION UNIVERSITY

Study: Macrobrachium rosenbergii Developmental Transcriptome

PRJNA174197 • SRP015487 • All experiments • All runs

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Developmental Transcriptome of the giant freshwater prawn Macrobrachium rosenbergii. Larvae and post larvae were pooled according to their developmental stages.

Sample: Larval sample#1/2

SAMN01180338 • SRS365108 • All experiments • All runs

Organism: Macrobrachium rosenbergii

Library:

Name: Larval sample#1/2

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Spot descriptor:

1 forward101 reverse

Pipeline: show...hide...

Program	Version
Velvet	2011
Oases	2011

Runs: 1 run, 592 spots, 116,100 bases, 206,280b

Run	# of Spots	# of Bases	Size	Published
SRR567391	592	116,100	206,280b	2013-09-17

ID:: 247941

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