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SRX22571127: scRNA-seq: Bag 3 Day 15
1 ILLUMINA (NextSeq 500) run: 68.1M spots, 5.7G bases, 2.5Gb downloads

Design: For analysis by 10X Genomics, tubes were defrosted and gently mixed, and 1.7 ml of the samples were transferred into an Eppendorf Lowbind tube and centrifuged at 4C for 3 min at 3000g. The PBS/methanol mix was discarded and replaced by 400 l of PBS. Cell concentration was measured using an iCyt Eclipse flow cytometer (SONY), based on forward scatter. Cell concentration ranged from 1044 cells ml-1 to 9855 cells ml-1. All concentrations were brought to 1000 cells ml-1 to target 7000 cells recovery, according to the 10X Genomics Cell Suspension Volume Calculator Table provided in the user guide. Cellular suspension was loaded onto Next GEM Chip G targeting 7000 cells and then ran on a Chromium Controller instrument to generate GEM emulsion (10x Genomics). Single-cell 3 RNA-seq libraries were generated according to the manufacturers protocol (10x Genomics Chromium Single Cell 3 Reagent Kit User Guide v3/v3.1 Chemistry) on different occasions: B4T19 and B7T17 in January 2020 and B3T15, B3T20, B4T13, B4T15, B4T20, B6T17, B7T16, and B7T18 in August 2020 with 12 cycles for cDNA amplification and 15 cycles for library amplification. Library concentrations and quality were measured using the Qubit dsDNA High Sensitivity Assay kit (Life Technologies, Carlsbad, CA). Libraries were pooled according to targeted cell number, aiming for a minimum 20,000 reads per cell. Pooled libraries were sequenced on using NextSeq 500 High Output kit (75 cycles).
Submitted by: Weizmann Institute of Science
Study: Aquacosm VIMS-Ehux Variation
show Abstracthide Abstract
The cosmopolitan coccolithophore Emiliania huxleyi is a unicellular alga that forms massive oceanic blooms covering thousands of square kilometers (Tyrrell and Merico 2004). The intricate calcite exoskeleton of E. huxleyi accounts for 1/3 of total marine CaCO3 production (Monteiro et al. 2016). E. huxleyi blooms are an important source of DMS, which is, by far, the most abundant volatile sulfur compound in the surface ocean and the best studied aerosol precursor (Simo 2001) with a significant climate-regulating role that enhances cloud formation (Alcolombri et al. 2015; Simo 2001). Biotic interactions that regulate the fate of these blooms play a profound role in determining carbon and nutrient cycling in the ocean and feedback to the atmosphere. Annual E. huxleyi spring blooms are frequently terminated following infection by a specific large dsDNA virus (EhV) that belongs to the Coccolithovirus group (Schroeder et al. 2002). Despite the huge ecological importance of host-virus interactions, the ability to assess their ecological impact is limited to questions that focus mainly on quantification of viral abundance and diversity in a reductionist manner.The project in which this dataset was collected is a holistic approach to untangle the complexity in alga-virus-bacterium interactions during an E. huxleyi bloom, their effect on the metabolome of the phycosphere, and their possible implications to C and S cycles. The project took place for 24 days, including daily sampling for various biological and physiochemical parameters. Flow cytometry was used to monitor different populations of phytoplankton, bacteria and virus-like particles (VLP). Additionally, physiochemical properties of the water such as salinity, temperature and nutrient concentrations were acquired. These data compose the contextual data for various scientific papers currently under preparation, coupled to sequencing efforts.
Sample: Fixed cells for single-cell RNA-seq
SAMN38317978 • SRS19578918 • All experiments • All runs
Library:
Name: B3T15
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC SINGLE CELL
Selection: cDNA
Layout: PAIRED
Runs: 1 run, 68.1M spots, 5.7G bases, 2.5Gb
Run# of Spots# of BasesSizePublished
SRR2687660368,052,3525.7G2.5Gb2024-02-20

ID:
30570586

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