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Sample GSM7794012

Query DataSets for GSM7794012

Status

Public on Sep 25, 2023

Title

Cells, UV day 10 2

Sample type

SRA

Source name

cells

Organism

Emiliania huxleyi

Characteristics

tissue: cells
cell line: CCMP3266
treatment: Constant UV

Treatment protocol

Continuous UV irradiation was achieved by placing a UV-emitting light source (Exo Terra Reptile UVB150, Hagen, Montreal, Canada) inside the algal growth chamber. Algal cultures experienced UV-A intensity of 0.5 w/m2, UV-B intensity of 0.07 w/m2 and UV-C intensity of 0.026 w/m2, measured using an ALMENO 2570 device (Ahlborn, Budapest, Hungary) placed within the Erlenmeyer. The UV-B intensity employed in this study was selected to replicate the UV-B radiation encountered at the ocean surface 29. The UV light-source was operating daily for 14 hours in parallel to the PAR light period, starting one hour after PAR illumination started, and ending one hour before PAR illumination ended. This irradiation regime was employed because in thought of imitating a simplified natural day cycle including a dawn and dusk period.

Growth protocol

The axenic algal strain of Emiliania huxleyi CCMP3266 was purchased from the National Center for Marine Algae and Microbiota (Bigelow Laboratory for Ocean Sciences, Maine, USA). Algae were grown in artificial sea water according to Goyet and Poisson 83 and supplemented with L1 medium according to Guillard and Hargraves 84, with the exception that Na2SiO3 was omitted following the cultivation recommendations for this strain. Algae were grown in standing cultures in borosilicate Erlenmeyers with an initial inoculum of 330 cells/ml, placed in a growth chamber at 18°C under a light/dark cycle of 16/8 hr. PAR intensity during the light period was 130 µmoles photonsm-2 s-1. Cultures volume was 50 ml except for cultures used to measure growth rates under vitamin D treatment (fig. S1) which were grown in 20 ml.

Extracted molecule

total RNA

Extraction protocol

Algal cultures were harvested for RNA extraction by centrifugation at 4000 rpm for 5 min at 18°C. RNA was extracted using the Isolate II RNA mini kit (Meridian Bioscience, London, UK) according to manufacturer instructions. Cells were ruptured in RLT buffer containing 1% β-mercapto-ethanol by bead beating for 5 min at 30 mHz. RNA was then treated with 3 µl Turbo DNAse (ThermoFisher, Waltham, USA) in a 50 µl reaction volume, followed by a cleaning step using RNA Clean & ConcentratorTM-5 kit (Zymo Research, Irvine, CA, USA) according to manufacturer instructions. RNA was used for generating transcriptomic data and qPCR analysis.
MARS-seq2.0 (Keren-Shaul H, Kenigsberg E, Jaitin DA, et al. MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing. Nat Protoc. 2019;14(6):1841-1862. doi:10.1038/s41596-019-0164-4)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

Day10-UV2

Data processing

UTAP (Kohen R, Barlev J, Hornung G, et al. UTAP: User-friendly Transcriptome Analysis Pipeline. BMC Bioinformatics. 2019;20(1):154. doi:10.1186/s12859-019-2728-2)
Assembly: GIZZ01000000
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample
Supplementary files format and content: tab-delimited text file includes UMI read counts for each sample
Supplementary files format and content: tab-delimited text file includes UMI counts for each sample and statistical analysis

Submission date

Sep 20, 2023

Last update date

Sep 25, 2023

Contact name

Or Eliason

E-mail(s)

ariadeiz@gmail.com

Organization name

The Weizmann Institute of Science

Street address

234 Hertzk