939c2973-3a9b-43dd-a3ad-739b659cf7ac - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005059 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This study reports Illumina Omni 2.5M genotyping chip data for 48 individuals from Aru, Mentawai, New Guinea and Sumba islands.
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Project description:High-coverage whole genome sequences were collected to study patterns of genomic variation across the broad geography of Indonesia and New Guinea. This region has experienced an extremely complex demographic history, including repeated bouts of admixture with archaic and modern human groups. This dataset reports whole genome sequences for 82 individuals from different populations from Mentawai, New Guinea, Sumatra and Sumba islands. Particular attention has been paid in the original study to genomic signals that are informative for population history, including admixture with archaic hominins and the role of modern human admixture during the late Pleistocene and Holocene.
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Project description:DNA methylation data were collected to study patterns of functional variation across the broad geography of Indonesia. The region has extremely diverse populations, with very different demographic histories and multiple genetic ancestries. This dataset reports Illumina Epic methylation chip data for individuals from three islands spanning this geographical region: Mentawai, Sumba and West Papua.
| EGAS00001003653 | EGA
Project description:Transcription data were collected to study patterns of functional variation across the broad geography of Indonesia. The region has extremely diverse populations, with very different demographic histories and multiple genetic ancestries. This dataset reports high-throughput RNA-sequencing data for individuals from three islands spanning this geographical region: Mentawai, Sumba and West Papua.
| EGAS00001003671 | EGA
Project description:This dataset contains 4 batches of Indonesian RNA-seq data from Mentawai, New Guinea and Sumba islands. One RNA-seq batch was prepared without Globin depletion, and three batches were Globin depleted using the Illumina Globin-Zero Gold Kit. There are 179 runs in total, including 119 unique samples. Dataset includes multiple batch control samples.
| EGAD00001005053 | EGA
Project description:Illumina single nucleotide polymorphism (SNP) array data were generated to study genome-wide patterns of genomic variation on Sumba and Timor, two small islands in eastern Indonesia. Both islands have a complex history from their initial settlement ~50,000 years ago, to admixture with Austronesian-speaking groups during the Neolithic farming expansion, and more recent intra-island gene flow and community interactions. As part of this detailed microgeographic study, we also collected associated cultural and linguistic information. The primary study location was Sumba, for which we genotyped SNPs in 235 individuals from eight communities that span the island, including groups that speak most of Sumba’s nine languages. Particular attention was paid to genomic data that are informative for recent aspects of population history, including reconstructions of past gene flow, socio-genetic interactions and possible signals of selection.
2016-07-14 | GSE76645 | GEO
Project description:High-coverage whole genome sequences were collected to study patterns of genomic variation across the broad geography of Indonesia and New Guinea. This region has experienced an extremely complex demographic history, including repeated bouts of admixture with archaic and modern human groups. We have sequenced the genomes of 161 individuals from 14 populations spanning this geographical region, from communities close to mainland Asia through to New Guinea.
| EGAD00001004156 | EGA
Project description:The present study reports the gene expression data of Mycobacterium tuberculosis H37Rv and H37RvΔdosSΔdosT (DKO) grown on 0.2 % acetate/glucose under aerobic/hypoxic conditions. Acetate was reported to be present in granulomas of Mycobacterium tuberculosis infected guinea pigs which are also hypoxic. By exposing Mycobacterium tuberculosis H37Rv and H37RvΔdosSΔdosT to different combinations of granulomatous stresses (acetate/glucose and aerobic/hypoxic conditions) alongwith other experimental data, we were able to delineate a new signaling pathway that activates DevR (DosR) regulon through Acetyl phosphate. The presence of two pathways highlights the importance of targeting DevR and not DevS/DosT for intercepting DevRST signalling cascade.
2019-01-01 | GSE117428 | GEO
Project description:High-coverage whole genome sequences were collected to study patterns of genomic variation across the broad geography of Papua New Guinea. This region has experienced an extremely complex demographic history, including repeated bouts of admixture with archaic and modern human groups. This dataset reports whole genome sequences for 163 individuals from different regions (Mt Wilhelm, Daru, Port Moresby). Particular attention has been paid in the original study to genomic signals that are informative for population history, and adaptive history, including admixture with archaic hominins and the role of modern human admixture during the late Pleistocene and Holocene.
| EGAS00001007085 | EGA
Project description:In this study we developed a guinea pig oligonucleotide microarray (GPOM) comprising of a total number of 45,220 features including 43,803 valid features from different mammalian species. These features are inclusive of 2971 newly annotated probes corresponding to 344 unique genes of guinea pig. As a case study, we utilized this array to examine the gene expression profile in guinea pig lungs in response to infection with Mycobacterium tuberculosis. Studying the global gene expression profile in guinea pigs allowed identification of the disease signature of pulmonary TB infection represented by several unique genes that are differentially regulated in this model. While, 1344 unique genes exhibited marked up regulation, 1856 genes were significantly down regulated. The newly developed tool not only finds its utility in studying the global gene expression profile associated with vaccination and/or M. tuberculosis infection in this highly useful animal model but would also be immensely useful in identification of new drug targets, testing of therapies, molecular genetic analysis for diseases other than tuberculosis as well. Genotypic Technology designed Custom Cavia porcellus 4x44k Gene Expression Array (Agilent-AMADID-019424) * In order to validate the GPOM developed in this study, we compared the gene expression profile of guinea pig lungs at 10 weeks post- M. tuberculosis infection with respect to that obtained from normal uninfected animals. To address this, guinea pigs were aerosol infected with M. tuberculosis, lungs were harvested at 10 weeks post-infection and RNA obtained from infected lungs was employed for cDNA synthesis and microarray hybridization. The gene expression was compared with the RNA sample obtained from the lungs of normal uninfected guinea pigs.
2012-10-01 | E-GEOD-32447 | biostudies-arrayexpress