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Transcriptome analysis in C.elegans from Parental P0 to F3 generations under hypoxic stress in both WT and hrde-1 mutant [RNA-seq]

ABSTRACT: The goal of RNA-seq is to identify the differentially expressed genes in the wild-type (WT) and hrde-1 mutant of C.elegans at the normoxia reared and hypoxia treatment conditions at P0 generation, and those maintained dysregulated genes in F1, F2 and F3 generation. Two biological replicates were assigned for each group and in total 32 groups were prepared for RNA-seq libraries with 500 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). We mapped about 20 - 30 million reads per sample to C.elegans (WS235) with RSEM pipline. Differential analysis were conducted using EdgeR. The significant genes were conducted by computing NB exact genewise tests with corrected p < 0.05.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE188269 | GEO | 2022/12/13

REPOSITORIES: GEO

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Small RNAseq analysis of C.elegans from Parental P0 to F3 generations under hypoxic stress in both WT and hrde-1 mutant [small RNA-seq]

Project description:The goal of small RNA-seq is to identify the differentially expressed small RNAs (microRNA, 22G RNA, piRNA, snoRNA) in the wild-type (WT) and hrde-1 mutant of C.elegans at the normoxia reared and hypoxia treatment conditions at P0 generation, and those small RNAs maintained dysregulation in F1, F2 and F3 generation.

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Transcriptome analysis in D. discoideium (AX2) in different developmental stages

Project description:The goal of RNA-seq is to identify the differential expressed genes in the wild-type D.discoideum at different developmental stages (vegetative, streaming, mound and fruiting bodyies). Two biological replicates were assigned for each group and in total 8 groups were prepared for RNA-seq libraries with 500 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). We mapped about 20 - 30 million reads per sample to D. discoideum with bowtie2 workflow. The analysis pipeline started with pseudo-alignment of the reads using kallisto, followed by building an index and quantification process, which generated h5 files containing the raw binary files for preliminary differential analysis in sleuth. Differential analysis were conducted in EdgeR. The significant genes were deducted by computing NB exact genewise tests with corrected p < 0.05. Our results showed stage-specific gene expression profiles in different developmental stages.

2021-04-21 | GSE137602 | GEO

A nuclear Argonaute promotes germline immortality and epigenetic inheritance across generations

Project description:dsRNA-mediated gene silencing (RNAi) can be inherited for multiple generations in C. elegans. To understand this process we conducted a genetic screen for animals defective for transmitting RNAi silencing signals to future generations. This screen identified the gene heritable RNAi defective (hrde)-1. hrde-1 encodes an Argonaute (Ago) that associates with siRNAs in germ cells of the progeny of animals exposed to dsRNA. In nuclei of these germ cells, HRDE-1 engages the Nrde nuclear RNAi pathway to promote RNAi inheritance, and directs H3K9me3 chromatin marks at RNAi targeted genomic loci. Under normal growth conditions, HRDE-1 associates with endogenously expressed small RNAs, which direct nuclear gene silencing in germ cells. In RNAi inheritance mutant animals, silencing is lost over generational time. Concurrently, RNAi inheritance mutant animals exhibit progressively worsening germline defects that ultimately lead to sterility. These results establish that the Ago HRDE-1 directs gene-silencing events in germ cell nuclei, which are required for multi-generational RNAi inheritance and immortality of the germ cell lineage. We propose that C. elegans use the RNAi inheritance machinery to transmit epigenetic information, accrued by past generations, into future generations to ensure immortality of the germ cell lineage. H3K9me3 Chip-IP for C. elegans strains nrde-3, nrde-4, glp-4. Small RNA-seq for small RNAs co-immunoprecipitated with HRDE-1

2012-07-30 | E-GEOD-38041 | biostudies-arrayexpress

Characterization of primary models of human trophoblast

Project description:To understand the human placenta development, we investigated the features of two trophoblast models, trophoblast organoids and trophoblast stem cells, with the aim of identifying which type of trophoblast in vivo they most closely resemble. To this end, we profiled the microRNAs from the two models by using the Bioo Nextflex protocol (NEXTFLEX Small RNA-seq Kit v3 for Illumina Platforms).

2021-10-18 | E-MTAB-10438 | biostudies-arrayexpress

A nuclear Argonaute promotes germline immortality and epigenetic inheritance across generations

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Expression Data from International C.elegans Experiment 1st

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Project description:We used several state-of-the-art site-centric chemoproteomics to systematically map three distinct types of redox forms (-SH, -SOH, and -SO2H) in C.elegans and quantify their dynamic changes in response to a short-term oxidative stress.

2021-01-28 | PXD018575 | Pride

C.elegans transcriptomic response to Mn exposure

Project description:Mn toxicity in C.elegans

| PRJEB52734 | ENA

Changes in small RNAs upon Viral infection of C.elegans

Project description:Attempt to identify small non-coding RNAs that change in levels as a result of viral infection of C.elegans

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HNF4α and TCF4 (TCF7L2) ChIPseq in Tet-On HCT116 inducible cell lines that express either the human HNF4α2 or HNF4α8 under the control of doxycycline (DOX) [ChIP-Seq]

Project description:Purpose: Aim of the study is to determine how many of the dysregulated genes in the RNAseq are direct targets of (P1) HNF4α2 and (P2) HNF4α8 and examine HNF4α and TCF4 binding in vivo. We performed ChIPseq on TCF4 in the absense or presence of DOX in the Tet-On inducible HCT116 HNF4α2 and HNF4α8 lines, and ChIPseq for HNF4α (a445 Ab) in the presence of DOX. Methods: HNF4α2 and HNF4α8 lines were induced with 0.3 μg/mL DOX for 24 hours. Samples were generated by deep sequencing, using the NEXTflex ChIPseq. Result: There were more HNF4α2 peaks than HNF4α8 peaks, with some common peaks bound by HNF4α2 and HNF4α8. Binding patterns were observed between HNF4α and TCF4. Conclusion: HNF4α2 can displace TCF4 better than HNF4α8 on AP-1 bound sites. Tet-On inducible HCT116 cell (HNF4α2 and HNF4α8) lines, treated with (0.3 μg/mL) or without DOX for 24 hours, were 50bp single-end sequenced using Illumina-compatible-NEXTflex ChIP kit (Bioo Scientific).

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