Koala buffy coat (ISIS # 504219) transcriptome raw and processed reads - SRA

SRX873837: Koala buffy coat (ISIS # 504219) transcriptome raw and processed reads
2 ILLUMINA (Illumina HiSeq 2000) runs: 150.5M spots, 30.3G bases, 17.3Gb downloads

Design: During routine health exams, whole blood was extracted from two individual koalas (ISIS #: 504219 and 510113). Buffy coat was extracted from the blood samples via Pasteur pipet after centrifugation for 20 min at 2000 rpm (~900x g). The buffy coat was then stored in TRIzol and frozen. The sample was shipped overnight on dry ice to Purdue University, where it was stored at -80 degrees Celsius. RNA was extracted using TRIzol (Life Technologies) and Direct-zol columns (Zymo Research) via manufacturer's instructions. Approximately 5 ug of RNA was used to create cDNA libraries using random hexamer primers according to the TruSeq RNA sample preparation manual (Illumina). The libraries were barcoded, pooled, and then sequenced on a lane of the Illumina HiSeq 2000 platform. The "raw" reads are those resulting from the previous steps. The "processed" were the result of further filtering. Specifically, the adaptor sequences were removed, the reads were filtered for quality (PHRED quality score > 20 and length > 30 bp), and putative ribosomal RNA reads were removed using DeconSeq and a custom vertebrate rRNA database.

Submitted by: Purdue University

Study: Immunomics of the koala (Phascolarctos cinereus)

PRJNA275238 • SRP053902 • All experiments • All runs

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We used Illumina sequencing of cDNA to characterize genes expressed in two different koala tissues of immunological importance, blood and spleen, with the intent if characterizing important genes related to infection and the immune response: toll-like receptors (TLRs), RIG-I like receptors (RLRs), major histocompatibility complex (MHC) genes, and koala retrovirus (KoRV).

Sample: ISIS_504219

SAMN03340167 • SRS843693 • All experiments • All runs

Organism: Phascolarctos cinereus adustus

Library:

Name: ISIS_504219_buffy_coat

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: PolyA

Layout: PAIRED

Spot descriptor:

1 forward102 reverse

Pipeline: show...hide...

Program	Version
DeconSeq	0.4.2

Runs: 2 runs, 150.5M spots, 30.3G bases, 17.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR1799715	74,229,251	14.9G	8.5Gb	2016-02-11
SRR1802483	76,254,207	15.4G	8.8Gb	2016-02-11

ID:: 1251628

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