NSM_2_1 - SRA

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SRX1456191: NSM_2_1
2 ILLUMINA (Illumina HiSeq 2000) runs: 25.1M spots, 4.7G bases, 2.3Gb downloads

Design: Strand-specific library preparation and sequencing A total of 3 μg RNA per sample was used in sequencing library construction using NEBNext UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA) following manufacturer’s recommendations. Briefly, mRNA was purified from total RNA using poly-T oligo magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in the NEBNext First Strand Synthesis Reaction Buffer. First strand cDNA was synthesized using random hexamer primer and M-MuLV reverse transcriptase (RNaseH-). The second strand cDNA was synthesized using DNA polymerase I and RNase H. For strand-specific sequencing, dTTP was replaced with dUTP during cDNA synthesis. After 397 converting overhanging ends into blunt ends and adenylation of 3’ ends of DNA fragments, NEBNext adaptors with hairpin loop structure were ligated to the cDNAs, and fragments of 150~200 bp were purified using AMPure XP system (Beckman Coulter, Sykesville, MD, USA). The samples were then treated with 3 μl USER Enzyme (Uracil-Specific Excision Reagent, NEB) at 37°C for 15 min followed by 5 min at 95°C before PCR amplification. The amplification was performed using Phusion high-fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer, and the PCR products were purified using an AMPure XP system. The quality of the libraries was assessed using Agilent Bioanalyzer 2100. Index-coded samples were clustered in a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After clustering, the libraries were sequenced in an Illumina Hiseq 2000 platform and 100 bp paired-end reads were generated.

Submitted by: NIH

Study: Plasmodium yoelii nigeriensis strain:NSM Raw sequence reads

PRJNA304182 • SRP066796 • All experiments • All runs

show Abstracthide Abstract

The rodent malaria parasite Plasmodium yoelii is an important animalmodel for studying host-parasite interaction and molecular basis of malaria pathogenesis.Although a draft genome of P. yoelii has been published, and assembled chromosomesare available publicly, errors in gene model prediction still exist. With the advances inDNA sequencing technologies and reduction in sequencing costs, genome-wide RNAsequencing (RNA-seq) has become an effective approach to study gene expression andgene expression regulation. Additionally, cDNA sequences can provide experimentalinformation to confirm or correct errors in the predicted gene models based on genomesequence.

Sample: The rodent malaria parasite Plasmodium yoelii is an important animal model for studying host-parasite interaction and molecular basis of malaria pathogenesis. Although a draft genome of P. yoelii has been published, and assembled chromosomes are available publicly, errors in gene model prediction still exist. With the advances in DNA sequencing technologies and reduction in sequencing costs, genome-wide RNA sequencing (RNA-seq) has become an effective approach to study gene expression and gene expression regulation. Additionally, cDNA sequences can provide experimental information to confirm or correct errors in the predicted gene models based on genome sequence.

SAMN04296701 • SRS1183776 • All experiments • All runs

Organism: Plasmodium yoelii nigeriensis

Library:

Name: NSM_2_1

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Spot descriptor:

1 forward101 reverse

Runs: 2 runs, 25.1M spots, 4.7G bases, 2.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR2966755	14,126,538	2.8G	1.6Gb	2015-12-15
SRR3001779	10,974,966	1.8G	684.5Mb	2015-12-29

ID:: 2058274

SRA

Sequence Read Archive

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