Dataset: Transcriptomic response of Emiliania huxleyi to HHQ

Name: NCBI accession numbers and related metadata from a study of transcriptomic response of Emiliania huxleyi to 2-heptyl-4-quinolone (HHQ)
Published: 2019-07-16
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.773272.1

Temporal Extent: 2018-06-20 - 2018-06-23

Project:

Collaborative Research: Building a framework for the role of bacterial-derived chemical signals in mediating phytoplankton population dynamics (HHQSignals)

Principal Investigator:

Kristen E. Whalen (Haverford College)

Co-Principal Investigator:

Elizabeth Harvey (Skidaway Institute of Oceanography, SkIO)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2019-07-16

Restricted:

Validated:

Yes

Current State:

Final no updates expected

NCBI accession numbers and related metadata from a study of transcriptomic response of Emiliania huxleyi to 2-heptyl-4-quinolone (HHQ)

Abstract:

NCBI accession numbers and related metadata from a study of transcriptomic response of Emiliania huxleyi to 2-heptyl-4-quinolone (HHQ). Sequences from this study are available at the NCBI GEO under accession series GSE131846 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE131846

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2019-07-16	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.773272.1	2020-07-31

Description

Sequences from this study are available at the NCBI GEO under accession series GSE131846 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?&acc=GSE131846

Methods & Sampling

Batch 2 L cultures of axenic Emiliania huxleyi strain CCMP2090 were grown in natural seawater-based f/2-Si medium (Guillard 1975) in sterile acid-washed polycarbonate bottles. Cultures were maintained on a 14:10 light (80 +/- 5 µmol photons m⁻² s⁻¹):dark cycle at 17.5 - 17.8 ᵒC. After 48 hr of growth, quadruplicate 2 L cultures were exposed to either 1 ng/ml, 10 ng/ml, or 100 ng/ml concentrations of 2-heptyl-4-quinolone (HHQ). Quadruplicate bottles were also exposed to dimethyl sulfoxide (DMSO) to serve as a vehicle control (final concentration 0.002% DMSO in all bottles). Cell biomass was collected 24 hr and 72 hr after treatment via centrifugation (9,000 RPM for 8 min at 4 ᵒC) of 400 ml of culture and total RNA extracted using the RNeasy Plus Mini Kit (Qiagen) following the manufacturer’s recommendations using 350 µl RLT plus buffer per sample and the optional centrifugation (14,000 RPM for 1 min) step to ensure membranes were dry prior to elution with 30 µl RNase free water. Eluent was reapplied to the membrane, and incubated for 8 min at room temperature before repeating the elution step to increase yield. Strand-specific RNAseq library construction was performed using the KAPA Stranded mRNA-Seq library preparation kit with KAPA mRNA capture beads (Kapa Biosystems) and sequenced on the NextSeq platform (Illumina) to generate 75 bp paired-end reads.

Data Processing Description

Sequenced reads were conservatively trimmed to remove adaptors, low-complexity and low-quality sequence, and rRNA reads (including chloroplast and mitochondria rRNA) using Trimmomatic (V0.38; Bolger et al. 2014) with a custom adapter file containing Emiliania huxleyi CCMP2090 rRNA sequences and the following settings: ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 MAXINFO:40:0.5 MINLEN:50. Read quality was examined before and after trimming using FastQC (V0.11.8; https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and MultiQC (V1.6; Ewels et al. 2016). Paired files produced by Trimmomatic were then concatenated prior to determination of transcript abundances using Salmon (V0.12.0; Patro et al. 2017) and the Ensembl (Kersey et al. 2017) gene predictions for Emiliania huxleyi CCMP1516 (the non-axenic form of CCMP2090; ftp://ftp.ensemblgenomes.org/pub/protists/release-41/fasta/emiliania_huxleyi/cdna/) as a transcript target index (k-mer size = 23). Salmon was run in the quasi-mapping mode with default settings and the following flags: --validateMappings and –gcBias. Quantification results from Salmon were examined using MultiQC (V1.6; Ewels et al. 2016) and then processed using the tximport R package with default settings (V1.10.0; Soneson et al. 2015) to prepare for gene-level analyses. Transcript and gene IDs were linked using the general feature format file for Emiliania huxleyi CCMP1516 available from Ensembl Genomes (ftp://ftp.ensemblgenomes.org/pub/protists/release-41/gff3/emiliania_huxleyi). Normalization and determination of significantly differentially abundant transcripts was preformed using the DESeq2 R package (V1.22.1; Love et al. 2014) using standard functions and workflows recommended by the authors. After estimation of size factors to normalize for differences in library sequencing depth and gene dispersion estimation using the biological replicates, tests for differential expression were carried out for each pairwise comparison of interest with the Wald test using a negative binomial generalized linear model. Logarithmic fold change (LFC) estimates were shrunken by calling the apeglm package (V1.6.0; Zhu et al. 2018) within DESeq2. The resulting p values were adjusted for multiple testing using the Benjamini-Hochberg (BH) procedure and transcripts with a BH-adjusted p value < 0.1 were deemed to be differentially abundant.

Data Files

File
e_hux_accessions.csv (Comma Separated Values (.csv), 15.74 KB) MD5:4d5ca5bc1735a81a731b72d9712425dc Primary data file for dataset ID 773272

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1657808
NSF Division of Ocean Sciences	OCE-1657818

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: llumina NextSeq500

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
series_accession	NCBI GEO identifier	unitless	accession_number
biosample_accession	NCBI BioSample identifier	unitless	accession_number
biosample_link	URL for SRA BioSample Page at NCBI	unitless	accession_number
sample_name	Sample name	unitless	sample_descrip
organism	NCBI taxonomy name	unitless	species
tax_ID	NCBI taxonomy ID	unitless	species
strain	Organism strain	unitless	sample_descrip
sample_type	Sample type	unitless	sample_descrip
biomaterial_provider	Name of the lab or PI or a culture collection identifier	unitless	laboratory
env_biome	Descriptor of the broad ecological contxt of a sample	unitless	site_descrip
samp_size	Amount of size of sample that was collected	unitless	cell_concentration
temp	Temperature of the sample at time of sampling	degrees Celsius	temp
light_level_umol_m2_s	Light level	microml photons m-2 s-1	irradiance
light_dark_hr	Duration of light and dark cycles	hours	duration
media	Type of growth medium used	unitless	treatment
collection_date	Date sample was collected; format: DD-Mmm-YYYY	unitless	date
geo_loc_name	Geographical origin of the sample	unitless	site
treatment	Treatment	unitless	treatment
time_elapsed	Time elapsed since treatment	hours	time_elapsed
bio_replicate	Biological replicate number	unitless	replicate

Status message

Database

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Dataset: Transcriptomic response of Emiliania huxleyi to HHQ