Marine metagenome
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:Whole genome sequence of single cells amplified with single droplet MDA
| PRJDB5352 | ENA
Project description:The genomic DNA of rearranged chromosome VIII (~900kb) of EC9 diploid strain was extracted from the gel of pulsed field gel electrophoresis (PFGE), and analyzed by array-CGH to identify it's amplified regions After PFGE, The ChrVIII DNA was purified from agarose gel and purified by column. Then the DNA was amplified by GenomePlex Whole Genome Amplification Kit for Array-comparative genomic hybridization.
2012-05-17 | E-GEOD-38034 | biostudies-arrayexpress
Project description:The genomic DNA of wild-type chromosome VIII of evolved EC9-7 cells was extracted from the gel of pulsed field gel electrophoresis (PFGE), and analyzed by array-CGH to identify its chromosomal composition Yeast genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit. After PFGE, The ChrVIII DNA was purified from agarose gel and purified by column. Then the DNA was amplified by GenomePlex Whole Genome Amplification Kit.
2011-11-13 | E-GEOD-33652 | biostudies-arrayexpress
Project description:Methanothermococcus single cell amplified whole genome sequencing
| PRJNA477509 | ENA
Project description:Single-cell human genome analysis using whole-genome amplified product is hampered by allele bias during amplification. Using an oligonucleotide SNP array, we examined the nature of the allele bias and its effect on the chromosomal copy number analysis. Keywords: single cell, copy number analysis, whole genome amplification, brain
2007-12-20 | GSE8567 | GEO
Project description:Single-cell genomics and single-cell transcriptomics have recently emerged as powerful tools to study the biology of single cells at a genome-wide scale. Here we describe a method that allows the integration of genomic DNA and mRNA sequencing from the same cell. We use this method to correlate DNA copy number variation to transcriptome variability among individual cells. First, hand-picked single cells are lysed and reverse transcribed using a poly-A primer including cell-specific barcodes, a 5' Illumina adapter and a T7 promoter overhang to convert mRNA to single stranded cDNA (ss cDNA). The gDNA and single stranded cDNA are then subjected to quasilinear whole genome amplification, as previously described, using an adapter with a defined 27 nucleotide sequence at the 5M-bM-^@M-^Y end followed by 8 random nucleotides. After 7 rounds of amplification, the gDNA and cDNA are copied to generate a variety of different short amplicon (0.5M-bM-^@M-^S2.5 kb) species, with a majority of amplicons containing adapter Ad-2 at both ends and a small fraction of cDNA derived amplicons containing Ad-2 at one end and Ad-1x at the other. Next, the sample is split into two tubes to further amplify gDNA and cDNA. The tube used to sequence gDNA is amplified using PCR. Following sonication, adapter Ad-2 removal, and cell-specific indexed Illumina library preparation, this half is used to sequence gDNA. The tube used to sequence cDNA is converted to double-stranded cDNA and amplified using in vitro transcription such that the amplified RNA (aRNA) is uniquely produced from cDNA but not gDNA. 3M-bM-^@M-^Y Illumina adapters are then ligated to the aRNA followed by reverse transcription and PCR, allowing quantification of mRNA.
2014-12-11 | E-GEOD-62952 | biostudies-arrayexpress
Project description:Whole genome sequence of single bacterial cells associated with corals
| PRJDB10112 | ENA
Project description:Single-cell human genome analysis using whole-genome amplified product is hampered by allele bias during amplification. Using an oligonucleotide SNP array, we examined the nature of the allele bias and its effect on the chromosomal copy number analysis. Experiment Overall Design: TB106, lymphoblastoid cell line; CMK11-5 and CMK86, cell line; WGA, whole-genome amplified from bulk DNA; SC, whole-genome amplified product from single cell. Genotype and copy number status were compared between non-amplified products and their single cell products.
2008-06-16 | E-GEOD-8567 | biostudies-arrayexpress
Project description:The genomic DNA of rearranged chromosome VIII (~900kb) of EC9 diploid strain was extracted from the gel of pulsed field gel electrophoresis (PFGE), and analyzed by array-CGH to identify it's amplified regions
2012-05-18 | GSE38034 | GEO
Project description:The goals of this study are to determine tissue composition of human lung organoids (hLOs) when maintained long-term (day 230). hLOs consist of alveolar epithelial cells, mesenchymal/endothelial cells, smooth muscle cells and immune cells. After dissociated hLOs, a target capture of 1x 104 cells was performed using the 10X Genomics Chromium Single Cell RNA sequencing. Briefly, single cell gel bead-in-emulsions(GEMs) are generated by passing cells with enzyme mix, partitioning oil, and barcoded gel beads by 10X Chromium chip. After GEM formation, the gel bead is dissolved and co-partitioned cell is lysed. Subsequently, reverse transcription (RT) occurs inside GEMs and barcoded full-length cDNA is generated. After RT, amplified cDNAs with barcode sequences (cell index and UMI) are pooled and single cell library is constructed using the Single Cell 3` Reagent Kit (v3 chemistry). The resulting library was sequenced on illumina HiseqX platform with 150bp paired end. Raw base calling files generated by illumine sequencing were demultiplexed based on the sample index read to generate FASTQ files using the 10X Genomics Cell Ranger (v3.0.2) pipeline. The raw reads were trimmed from the 3’ end to get the recommended number of cycle for read pairs (read1: 28bp; read2 : 91bp). The trimmed reads were mapped to the hg38 reference human genome with subsequent analysis, including filtering, barcode counting, and UMI counting. The resulting data were used to generate the multidimensional feature-barcode matrix using the CellRanger count with default parameters.
2020-01-03 | GSE142838 | GEO