4 resultados para whole genome amplification

em Publishing Network for Geoscientific


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General global cooling over the Neogene has been modulated by changes in Earth's orbital parameters. Investigations of deep-sea sediment sequences show that various orbital cycles can dominate climate records for different latitudes or for different time intervals. However, a comprehensive understanding of astronomical imprints over the entire Neogene has been elusive because of the general absence of long, continuous records extending beyond the Pliocene. We present benthic foraminiferal d18O and d13C records over the past 23 Ma at Ocean Drilling Program Site 1148 in the northern South China Sea and construct an astronomically tuned timescale (TJ08) for these records based on natural gamma radiation and color reflectance data at this site. Our results show that a 41 ka cycle has dominated sediment records at this location over the Neogene, displaying a linear response to orbital forcing. A 100 ka cycle has also been significant. However, it is correlated nonlinearly with Earth's orbital variations at the 100 ka band. The sediment records also display a prominent 405 ka cycle. Although this cycle was coherent with orbital forcing during the Oligocene and the early Miocene, it was not coherent with Earth's orbital variations at the 405 ka band over the whole Neogene. Amplification of Northern Hemisphere and Southern Hemisphere glaciation since the middle Miocene may be responsible for this change in sedimentary response. Our benthic foraminifera d18O and d13C records further exhibit amplitude variations with longer periods of 600, 1000, 1200, and 2400 ka. Apparently, these cycles are nonlinear responses to insolation forcing.

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The present data set provides an Excel file in a zip archive. The file lists 334 samples of size fractionated eukaryotic plankton community with a suite of associated metadata (Database W1). Note that if most samples represented the piconano- (0.8-5 µm, 73 samples), nano- (5-20 µm, 74 samples), micro- (20-180 µm, 70 samples), and meso- (180-2000 µm, 76 samples) planktonic size fractions, some represented different organismal size-fractions: 0.2-3 µm (1 sample), 0.8-20 µm (6 samples), 0.8 µm - infinity (33 samples), and 3-20 µm (1 sample). The table contains the following fields: a unique sample sequence identifier; the sampling station identifier; the Tara Oceans sample identifier (TARA_xxxxxxxxxx); an INDSC accession number allowing to retrieve raw sequence data for the major nucleotide databases (short read archives at EBI, NCBI or DDBJ); the depth of sampling (Subsurface - SUR or Deep Chlorophyll Maximum - DCM); the targeted size range; the sequences template (either DNA or WGA/DNA if DNA extracted from the filters was Whole Genome Amplified); the latitude of the sampling event (decimal degrees); the longitude of the sampling event (decimal degrees); the time and date of the sampling event; the device used to collect the sample; the logsheet event corresponding to the sampling event ; the volume of water sampled (liters). Then follows information on the cleaning bioinformatics pipeline shown on Figure W2 of the supplementary litterature publication: the number of merged pairs present in the raw sequence file; the number of those sequences matching both primers; the number of sequences after quality-check filtering; the number of sequences after chimera removal; and finally the number of sequences after selecting only barcodes present in at least three copies in total and in at least two samples. Finally, are given for each sequence sample: the number of distinct sequences (metabarcodes); the number of OTUs; the average number of barcode per OTU; the Shannon diversity index based on barcodes for each sample (URL of W4 dataset in PANGAEA); and the Shannon diversity index based on each OTU (URL of W5 dataset in PANGAEA).