RNA-Seq of seawater: Coastal DCEWAF Timepoint 6 - SRA

SRX6614281: RNA-Seq of seawater: Coastal DCEWAF Timepoint 6
1 ILLUMINA (Illumina HiSeq 2500) run: 48.2M spots, 7.3G bases, 5Gb downloads

Design: Filtered seawater samples were homogenized for 2 min in TE buffer (1mM EDTA, 10mM Tris; pH 6.3) with ~1g of sterilized 0.1mm diameter zirconia/silica beads. After bead beating, crude extracts were amended with two volumes of chilled (4) denaturing buffer (4M guanidine thiocyanate, 50mM Tris, 10mM EDTA, 1% w/v N-lauroylsarcosine, 1% ?-mercaptoethanol) and pelleted via centrifugation (4500xg for 5 min at 4). The resulting supernatant was extracted with an equal volume of phenol:chloroform:isoamyl alcohol (25:24:1, pH 6.6), followed by a second extraction with chloroform:isoamyl alcohol (24:1). Nucleic acids were purified from these extracts via an overnight isopropanol precipitation with 3M sodium acetate (pH 6.0) and a subsequent 70% ethanol wash, followed by resuspension in 100 of TE buffer. Genomic DNA was eliminated from RNA samples with TURBO DNAse (Ambion) followed by purification with MEGAclear Transcription Clean-up kits (Ambion). The resulting purified total RNA extracts were processed with MICROBExpress kits (Ambion) to reduce the amount of 16S and 23S rRNA transcripts within the samples and then sent to the University of Delaware DNA Sequencing & Genotyping Center (Newark, DE, USA) for Illumina HiSeq 2500 sequencing (SINGLE-end 150bp reads).

Submitted by: Texas A&M University

Study: ADDOMEx Consortium: Gulf of Mexico, Open Ocean (GOMOO) and Coastal Water (GOMCOAST) Metatranscriptomes

PRJNA557240 • SRP216817 • All experiments • All runs

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Here we describe the microbial metatranscriptomic response to water accommodated fraction of oil with and without the dispersant Corexit over time in offshore and coastal seawater collected from the northwestern Gulf of Mexico.

Sample: Coastal-72hours-DCEWAF

SAMN12392216 • SRS5178287 • All experiments • All runs

Organism: seawater metagenome

Library:

Name: M4_T6_DCEWAF_metaT

Instrument: Illumina HiSeq 2500

Strategy: RNA-Seq

Source: METATRANSCRIPTOMIC

Selection: Inverse rRNA

Layout: PAIRED

Runs: 1 run, 48.2M spots, 7.3G bases, 5Gb

Run	# of Spots	# of Bases	Size	Published
SRR9860486	48,163,002	7.3G	5Gb	2019-07-30

ID:: 8724872

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