SNPArray_TW
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010002424 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:The compressed file contains plink format file for the Affymetrix Human Origins SNP array data of 260 individuals generated and analyzed in Liu et al 2020 study of 22 ethnolinguistic groups in Vietnam.
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Project description:The compressed file contains plink format files for the Affymetrix Human Origins SNP array data of 208 Angolan individuals
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Project description:postQC genotype data from the Affymetrix AxiomTM HGCoV2 1 array in plink binary format. QC was carried out using PLINK v1.9
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Project description:Temporal analysis of Irf4 and PU.1 genome binding during B cell activation and differentiation in vitro using antigen (NP-Ficoll) CD40L and IL-2/4/5 cytokines (see Molecular Systems Biology 7:495 for details of cellular system). The results provide insight in the target genes and binding specificity of IRF4 and PU.1 during coordination of different programs of B cell differentiation. Regrettably three of the FASTQ raw sequence files in our study were corrupted during storage. FASTQ data from our experimental and control groups are available for download via GEO SRA; however, two groups are missing select raw sequence files. These include one PU.1 Day 3 group file (Sample GSM1133499) and two of four input files used to generate a concatenated “super” input file (Sample GSM1133490); the raw data provided for input consists of the two input files recovered. Importantly, FASTA sequences for both of these datasets are available as supplementary data through GEO, and we can make available upon request (rsciamma@uchicago.edu) all files in our study in the ELAND-extended alignment format. Please note that GEO no longer supports this format.
2013-05-04 | GSE46607 | GEO
Project description:We describe "Aird", an opensource and computation-oriented format with controllable precision, flexible indexing strategies, and high compression rate. Aird provides a novel compressor called Zlib-Diff-PforDelta (ZDPD) for m/z data. Compared with Zlib only, m/z data size is about 55% lower in Aird on average. With the high-speed decoding and encoding performance brought by the Single Instruction Multiple Data(SIMD) technology used in the ZDPD, Aird merely takes 33% decoding time compared with Zlib. We used the open dataset HYE, which contains 48 raw files from SCIEX TripleTOF 5600 and TripleTOF6600. The total file size is 206GB as the vendor format. The total size increases to 854GB after converting to mzML with 32-bit encoding precision. While it takes only 189GB when using Aird. Aird uses JavaScript Object Notation (JSON) for metadata storage. Aird-SDK is written in Java and AirdPro is a GUI client for vendor file converting which is written in C#. They are freely available at https://github.com/CSi-Studio/Aird-SDK and https://github.com/CSi-Studio/AirdPro.
2021-04-12 | PXD025142 | Pride
Project description:S2 cells were infected with FHV deltaB2 particle and the S2 cells were harvested to isolate total RNA at 96 hpi. Small RNAs were separated on a denaturing 15% polyacrylamide gel. Ligation to adapters requires 5' monophosphate and 3' OH. Note: The base quality (.qual) file corresponding to the fasta format (.fna) file linked to Sample GSM306489 is unavailable.
2008-10-16 | GSE12527 | GEO
Project description:Only a few scattered groups with oral traditions of Khoe-San hunter-gatherer ancestry remain in southeastern Africa. We investigate genomic variation of remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published datasets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu-speakers. Specifically, we found that the Lake Chrissie San are closely related to current southern San groups (i.e. the Karretjie People). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. Samples were genotyped on the Illumina Omni2.5M (HumanOmni25-8v1-2_A1) SNP chip. Results were analyzed using the software GenomeStudio 2011.1 and the data were exported to Plink format, aligned to Human Genome build version 37.
2016-09-21 | E-MTAB-5119 | biostudies-arrayexpress