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Denisova Cave South Chamber - sediment DNA

ABSTRACT: Sequencing of mtDNA captures of sediments from the Pleistocene layers of the South Chamber of Denisova Cave.

PROVIDER: PRJEB80323 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	ERR14153000.fastq.gz	Fastqsanger.gz
	ERR14153000_1.fastq.gz	Fastqsanger.gz
	ERR14153000_2.fastq.gz	Fastqsanger.gz
	ERR14153100.fastq.gz	Fastqsanger.gz
	ERR14153100_1.fastq.gz	Fastqsanger.gz

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Denisova Cave sediment DNA

Project description:Sequencing of mtDNA captures of sediments from the Pleistocene layers of Denisova Cave.

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Project description:Samples were used for a study on the ability to use deamidation rates to assess relative chronology at Denisova Cave. The majority of the samples for the study were analyzed using peptide mass fingerprinting (data publicly available - see associated manuscript for details). 15 samples from 7 layers in Denisova Cave were chosen for LC-MS/MS analysis. Prior to analysis samples were demineralized in hydrochloric acid, gelatinized in ammonium bicarbonate, digested with trypsin, and desalted with C18 ZipTips. Data was processed using Byonic with SwissProt as the database to obtain a focused database of just the proteins present in the samples. This focused database was combined with curated collagen sequences (database presented here) and used for analysis with MaxQuant and deamiDATE. For more details see associated publication. Provided here are the raw files, peak lists for Byonic, results files for Byonic, sequence database (focused database and currated collagen sequences), metadata file with information linking the file names here to the file names of the peptide mass fingerprinting samples, and a zip file of the Max Quant and deamiDATE results.

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