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Small RNA analysis of Piwi-induced permanently silent transgenic strains

ABSTRACT: Small RNA libraries from total RNA isolated from adult animals

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE39226 | GEO | 2012/07/11

SECONDARY ACCESSION(S): PRJNA170254

REPOSITORIES: GEO

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Small RNA analysis of Piwi-induced permanently silent transgenic strains

Project description:Small RNA libraries from total RNA isolated from adult animals Small RNA libraries were derived from genetically identical strains carrying a 21Usensor transgene in single copy. In one strain the transgene has become permanently silent and is not reactivated by RNAi against prg-1 (RNAe). In the other the transgene reactivates upon RNAi against prg-1.

2012-07-11 | E-GEOD-39226 | biostudies-arrayexpress

Small RNA libraries

Project description:Small RNA libraries

| PRJNA478199 | ENA

Small RNA sequencing in mutant strains of C. elegans infected by the Orsay virus

Project description:Background information: According to our observations, cde-1 (tm1021) null C. elegans animals show increased susceptibility to the Orsay virus (which has a bipartite positive RNA genome), compared to WT (N2 strain). Viral infection seems limited to intestinal cells. CDE-1 is a terminal uridylyltransferase (TUT). TUTs have been shown to promote RNA decay by 3’ end uridylation in various contexts and organisms. We hypothesize that CDE-1 serves as an antiviral factor by uridylating the viral RNA genome. Aims: We question small RNA populations in cde-1 mutants versus WT after two days of infection by the Orsay virus. Methods: Approximately 200 C. elegans animals were infected for 48 hours from the L2 stage to the adult stage with 20 µl filtrate of the Orsay virus on 50mm plate seeded with HB101 bacteria, in biological duplicates, for the following genetic backgrounds: N2 (+), drh-1 (ok3495), rde-1 (ne219), cde-1 (mj414), cde-1 (tm1021), cde-1 (tm1021);drh-1 (ok3495), cde-1 (tm1021);rde-1 (ne219). Animals were then washed in M9 and resuspended in 1 ml TRIsure (Bioline). Samples were freeze-thaw three times using liquid nitrogen and RNA purification was performed according to Bioline’s guidelines. Purified RNA was either directly used for library preparation (5’ dependent libraries) or was first submitted to 5’ polyphosphatase treatment (5’ independent libraries) as in Ashe, et al. 2013. sRNA libraries were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (with size selection between 20 and 35 nt, adapters excluded) and deep sequencing was produced with an Illumina HiSeq machine (single read 36).

2019-04-12 | GSE80169 | GEO

The Ino80 complex prevents invasion of euchromatin into silent chromatin

Project description:Purpose: We want to know whether Ino80C contribute to chromatin silencing at both euchromatin and heterochromatin Methods: All yeast cells were collected in exponential phase. Total RNA was extracted with phenol, digested with DNase and further purified by Trizol. Libraries of mRNA were prepared with Illumina TruSeq RNA Sample Prep Kits v2 or stranded RNA Sample Prep Kits. Libraries were sequenced on Illumina HiSeq 2000. ChIP DNA were purified through chromatin immunoprecipitation using an Arp5, H3K79me3 and H3K4me3 antibody. Libraries were prepared with a KAPA LTP kit and sequenced using the Illumina HiSeq 2000 platform. Conclusion: Our ChIP-Seq and mRNA-Seq data show that Ino80C contributes to silent chromatin in both euchromatin an heterochromatin

2015-01-22 | GSE52000 | GEO

RNA associating with PIWI proteins in Bombyx mori BmN4 cells

Project description:RNAs associating with PIWI proteins were Immunoisolated from BmN4 cells. Sequence libraries were generated with NEBNext Small RNA Library Prep Set for Illumina(NEB). Libraries were sequenced using Illumina MiSeq (single-end, 51 cycles).

2020-09-02 | GSE150444 | GEO

Cloning of the quail PIWI gene and characterization of PIWI binding to small RNAs.

Project description: Not available

| S-EPMC3526641 | biostudies-literature

small RNA-seq from induced pluripotent stem cell (ENCSR722POQ)

Project description:The libraries contained in this experiment come from independent growths of an induced pluripotent cell line, iPSC. They are stranded SE101 Illumina Hi-Seq RNA-Seq libraries from rRNA-depleted Total RNA < 200 nucleotides in size that was pre-treated with TAP prior to cloning. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-03-18 | GSE78438 | GEO

Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi

Project description:Various small RNA libraries from purified microtubules or Xiwi immunoprecipitates or total extract from X.tropicalis or X.laevis egg extract. Various small RNA libraries from single X.tropicalis eggs. Analysis of this series of files is described in the manuscript "Systematic and single cell analysis of Xenopus Piwi-interacting RNAs and Xiwi".

2009-09-01 | GSE15556 | GEO

Identification of the molecular basis of anti-cancer effect of Huaier.

Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None. Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes. For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..

| 2612481 | ecrin-mdr-crc

Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.

Project description:RNA libraries from immunoprecipitates of Tdrd1, Ziwi and Zili, total testis RNA, total RNA from 3 week old wild-type and tdrd1 mutant gonads.

2011-08-31 | GSE29418 | GEO

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