Ontology highlight
ABSTRACT:
PROVIDER: PRJNA554355 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:MicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique explicitly suitable for profiling of known and novel microRNAs. A modification to the small-RNA expression kit (SREK, Ambion) library preparation method for the SOLiD sequencing platform is described to generate microRNA sequencing libraries that are compatible with the Illumina Genome Analyzer. High quality sequencing libraries can successfully be prepared from as little as 100 ng small RNA enriched RNA. An easy to use perl-based analysis pipeline called E-miR was developed to handle the sequencing data in several automated steps including data format conversion, 3' adapter removal, genome alignment and annotation to non-coding RNA transcripts. Both the sample preparation and E-miR pipeline were successfully used to determine cardiac enriched microRNA expression in stage 16 chicken embryos. Comparing miRNA expression profiles for whole Chicken Embryo and isolated Heart tubes at developmental stage HH16
2010-12-21 | E-GEOD-20757 | biostudies-arrayexpress
Project description:The goal of this study was to compare wild-type adult homeostatic lung epithelium to Hopx-creERT2-induced Yap/Taz KO in adult AT1 cells. Three adult mice with identical genotypes and either sex were pooled after fluorescence-activated cell sorting and loaded into the 10X Chromium scRNA sequencing library generation pipeline.
2021-05-20 | GSE164422 | GEO
Project description:Setup and optimisation of a high throughput pipeline for ChIPseq. The protocol used is ChIP carried out using the Agilent Bravo robot with subsequent Ilumina sequencing library preparation.This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2013-02-12 | E-ERAD-77 | biostudies-arrayexpress
Project description:We obtained HBV-infected liver tissues from liver surgery(AST<40) and liver transplantation(AST>40) to perform next-generation sequencing (NGS). Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2000 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results, we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of HBV-infected liver from liver surgery(AST<40) and liver transplantation(AST>40).
2023-04-05 | GSE208637 | GEO
Project description:We enriched circulating and hepatic CD161N, CD161P and MAIT cells through flow sorting from heathy donors and HBV-infected patients to perform next-generation sequencing (NGS). Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina novaseq 6000 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results, we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of CD161N,CD161P and MAITcells from healthy donors and HBV-infected patients.
2023-04-05 | GSE208535 | GEO
Project description:MicroRNAs are small non-coding RNA transcripts that regulate post-transcriptional gene expression. The millions of short sequence reads generated by next generation sequencing technologies make this technique explicitly suitable for profiling of known and novel microRNAs. A modification to the small-RNA expression kit (SREK, Ambion) library preparation method for the SOLiD sequencing platform is described to generate microRNA sequencing libraries that are compatible with the Illumina Genome Analyzer. High quality sequencing libraries can successfully be prepared from as little as 100 ng small RNA enriched RNA. An easy to use perl-based analysis pipeline called E-miR was developed to handle the sequencing data in several automated steps including data format conversion, 3' adapter removal, genome alignment and annotation to non-coding RNA transcripts. Both the sample preparation and E-miR pipeline were successfully used to determine cardiac enriched microRNA expression in stage 16 chicken embryos.
2010-12-21 | GSE20757 | GEO
Project description:The goal of this study is to investigate the effect of ABCB6 inhibition on the transcriptome level of melanoma cell line MNT-1. We performed next-generation sequencing (NGS) on both ABCB6 depleted MNT-1 cells (shABCB6) and unknocked control cells (CTRL). Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2500 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results，we performed the GO and KEGG pathway enrichment analysis. That might suggest the key role of ABCB6 in modulating melanocyte development.
2021-03-06 | GSE168345 | GEO
Project description:With the recent advancements in genome editing, next generation sequencing (NGS), and scalable cloning techniques, scientists can now conduct genetic screens at unprecedented levels of scale and precision. With such a multitude of technologies, there is a need for a simple yet comprehensive pipeline to enable systematic mammalian genetic screening. In this study, we develop novel algorithms for target identi fication and a toxin-less Gateway cloning tool, termed MegaGate, for library cloning which, when combined with existing genetic perturbation methods and NGS-coupled readouts, enable versatile engineering of relevant mammalian cell lines. Our integrated pipeline for Sequencing-based Target Ascertainment and Modular Perturbation Screening (STAMPScreen) can thus be utilized for a host of cell state engineering applications.
2021-08-14 | GSE182088 | GEO
Project description:We describe a series of computational pipelines for the in silico analysis of small RNAs (sRNA) produced in response to viral infections in plants. Our workflow is primarily focused on the analysis of sRNA populations derived from known or previously undescribed viruses infecting host plants. Furthermore, we provide an additional pipeline to examine host-specific endogenous sRNAs activated or specifically expressed during viral infections in plants. We present some key points for a successful and cost-efficient processing of next generation sequencing sRNA libraries, from purification of high quality RNA to guidance for library preparation and sequencing strategies. We report a series of free available tools and programs as well as in-house Perl scripts to perform in-house sRNA-seq data mining. A multi-step analysis pipeline is extensively detailed so previous bioinformatic background is not required, but experience with basic Unix commands is desirable.
2017-10-12 | GSE104799 | GEO
Project description:The present study is expected to reveal regulatory network of small RNAs under drought in Sorghum (Sorghum bicolor (L.) Moench). Sorghum genotype drought tolerant (DT) and drought susceptible (DS) were grown at 28-32 degrees C day/night temperature with 12/12 h light/dark period in the phytotron glass house. The fully opened uppermost leaves from control and drought stressed seedlings were sampled and stored at -80 degrees C, and used for generation of a small RNA library. Total RNA was isolated from the leaves using the TRIzol reagent (Invitrogen, USA). Small RNA sequencing libraries were prepared using Illumina Truseq small RNA Library preparation kit following manufacturer's protocol and these libraries were sequenced on GAIIx platform (Illumina Inc., USA). Small RNA reads contaminated with poor-quality and adaptor sequences were trimmed by using the UEA sRNA workbench 2.4- Plant version sequence file pre-processing (http://srna-tools.cmp.uea.ac.uk/). Then, all unique reads were submitted to the UEA sRNA toolkit-Plant version miRCat pipeline (http://srna-tools.cmp.uea.ac.uk/) to predict novel miRNAs from high-throughput small RNA sequencing data.
2014-04-15 | E-MTAB-1630 | biostudies-arrayexpress