RNA metatranscriptome of Gulf of Maine microbes collected on 2017-11-... - SRA

SRX15836833: RNA metatranscriptome of Gulf of Maine microbes collected on 2017-11-02
1 ILLUMINA (NextSeq 500) run: 127.1M spots, 24.4G bases, 8.3Gb downloads

Design: cDNA libraries for Illumina shotgun sequencing were generated with the KAPA RNA HyperPrep (Roche Sequencing). The library was size-selected with BluePippin (Sage Science) set for 370 bp tight and quantified with a Tapestation (Agillent). This library was sequenced with NextSeq 500 (Illumina) in 2150bp mode. After sequencing, reads from the cDNA library were initially trimmed with trimmomatic (settings -phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:75). Reads matching the H. sapiens reference assembly GRCh38 and a local database of WGA-X reagent contaminants (Stepanauskas, R. et al. Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nat. Commun. 8, 84 (2017) doi:10.1038/s41467-017-00128-z) (95% identity of 100 bp alignments), as well as low complexity reads (containing <5% of any nucleotide) were removed. The remaining reads were merged with bbmerge using the following settings: k=40, extend2=60, iterations=5, loose=t, qtrim2=t.

Submitted by: Bigelow Laboratory for Ocean Sciences

Study: Gulf of Maine single cell genome to phenome

PRJNA846736 • SRP383251 • All experiments • All runs

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This study links the phenome of individual cells with their genome through the application of indexed FACS sorting and sequencing of individual cells. In brief single cells from the environment were sorted and phenotypic data was collected using a flow cytometer. Isolated cells were then individually sequenced and linked back to the measured phenomes. This was then used to investigate differences between different species and between cells of the same species.

Sample: RNA metatranscriptome from coastal waters in the Gulf of Maine

SAMN29250182 • SRS13527801 • All experiments • All runs

Organism: seawater metagenome

Library:

Name: GoM_20171102_Metatranscriptome

Instrument: NextSeq 500

Strategy: RNA-Seq

Source: METATRANSCRIPTOMIC

Selection: PCR

Layout: PAIRED

Runs: 1 run, 127.1M spots, 24.4G bases, 8.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR19792882	127,052,549	24.4G	8.3Gb	2022-10-12

ID:: 22495566

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