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Reproducibility of standard and micro-scaled H3K4me2 ChIP-Seq assay in mouse derived lymphoblastic cell line (D10.G4.1 cells, ATCC)

ABSTRACT: To estimate the reproducibility of standard and micro-scaled H3K4me2 ChIP-Seq assay we performed the genome-wide correlation analysis of H3K4me2 enrichment patterns from 7 independent standard ChIP-Seq assays (2 million D10 cells), and micro-scaled ChIP-Seq 100,000 cells sample –(N=12), 10,000 cells sample–(N=3), and 1000 cell sample – (N=4)

ORGANISM(S): Mus musculus

PROVIDER: GSE53644 | GEO | 2014/07/05

SECONDARY ACCESSION(S): PRJNA232546

REPOSITORIES: GEO

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Reproducibility of standard and micro-scaled H3K4me2 ChIP-Seq assay in mouse derived lymphoblastic cell line (D10.G4.1 cells, ATCC)

Project description:To estimate the reproducibility of standard and micro-scaled H3K4me2 ChIP-Seq assay we performed the genome-wide correlation analysis of H3K4me2 enrichment patterns from 7 independent standard ChIP-Seq assays (2 million D10 cells), and micro-scaled ChIP-Seq 100,000 cells sample M-bM-^@M-^S(N=12), 10,000 cells sampleM-bM-^@M-^S(N=3), and 1000 cell sample M-bM-^@M-^S (N=4) Examination of H3K4me2 histone modifications in mouse derived lymphoblastic cell line (D10.G4.1 cells, ATCC).

2014-07-05 | E-GEOD-53644 | biostudies-arrayexpress

Mus musculus

Project description:Reproducibility of standard and micro-scaled H3K4me2 ChIP-Seq assay in mouse derived lymphoblastic cell line (D10.G4.1 cells, ATCC)

| PRJNA232546 | ENA

D10 Stereocilia Membrane Enrichment

Project description:Through its activity in stereocilia, MYO7A (myosin VIIA) is essential for hair cell function in the inner ear. Utilizing multiple stages of immunoaffinity enrichment, we have developed a strategy that allows us to partially purify stereocilia membranes from thousands of chick inner ears and isolate low-abundance MYO7A protein complexes from those membranes. The D10 stereocilia membrane enrichment protocol involves density centrifugation steps and immuno-enrichment of stereocilia using the D10 antibody, directed against the major stereocilia transmembrane protein PTPRQ. The data in this submission document the effectiveness of the enrichment procedure.

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Vaccinia virus D10 has broad decapping activity that is regulated by mRNA splicing

Project description:Vaccinia virus (VACV) encodes decapping enzyme D10 that suppresses gene expression by removing the protective 5’ cap off mRNAs, rendering them susceptible to degradation by cellular exonucleases. Here, we use RNA-seq to profile the repertoire of transcripts targeted by D10 in isolation as well as in the context of VACV infection. We found that D10 is a broadly acting decapping enzyme and targets the vast majority of human transcripts. Notably, we found that the splicing architecture of a gene influences how robustly its corresponding transcript is targeted by D10, with transcripts derived from intronless genes being less susceptible to D10 activity. Since all viral genes are intronless, and some viral transcripts are uncapped, D10 preferentially targets host transcripts over viral transcripts. The disproportionate activity of D10 towards host transcripts may help the virus restrict host innate immune response and shift the translational resources towards viral protein synthesis.

2022-02-02 | GSE185520 | GEO

Plasmodium falciparum D10

Project description:Plasmodium falciparum strain D10

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Yeast D10 Small ~ WT San I

Project description:Transcriptional profiling of parental S. cerevisiae San I cells in comparison with its translocant derivative D10 Small strain. The latter strain was obtained using Bridge Induced translocation technique between DUR3 gene (Chromosome VIII) and ADH1 gene (Chromosome XV), and exhibited an abnormal phenotype comprising elongated buds and multi-budded, unevenly nucleated pseudo-hyphae. Goal was to demonstrate how chromosomal translocations can influence gene expression of translocant and other chromosomes. Two-condition experiment, direct comparison of Saccharomyces cerevisiae D10 small (4 biological replicates) vs. pooled WT San I (reference) cells.

2010-09-03 | E-GEOD-23966 | biostudies-arrayexpress

Yeast D10 Small ~ WT San I

2010-09-03 | GSE23966 | GEO

Brassica rapa strain:S7 D10 | cultivar:FPsc S7 D10

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alpha proteobacterium SCGC AAA028-D10

Project description:alpha proteobacterium SCGC AAA028-D10 overview

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Transcription profiling of human cells line with different D10 values to assay radiosensitivity

Project description:Expression analysis between cell lines that show different "D10" which is one of the parameters for radiosensitivity. This experiment includes three experimental factors: cell line, irradiation dose and time after irradiation.

2006-01-06 | E-MEXP-272 | biostudies-arrayexpress

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