Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Huntington’s disease-specific mis-splicing unveils key effector genes and altered splicing factors

ABSTRACT: RNA-seq analysis of 6 human and 6 mouse striatum samples: 3 control human subjects and 3 Huntington's disease patients, together with 3 control (wild type) mice and 3 early symptomatic R6/1 mice. The RNA-seq libraries were prepared with KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Roche) and were sequenced on HiSeq 2500 (Illumina, Inc) with a read length of 2x101bp.

PROVIDER: PRJEB44140 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR5670940_1.fastq.gz	Fastqsanger.gz
	ERR5670940_2.fastq.gz	Fastqsanger.gz
	ERR5670950_1.fastq.gz	Fastqsanger.gz
	ERR5670950_2.fastq.gz	Fastqsanger.gz
	ERR5670941_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Transcriptome response of Chlamydomonas reinhardtii exposed to methylmercury (MeHg)

Project description:This study aims at investigating the effects of methylmercury on a microalga using a transcriptomic approach. Algal cells were exposed two hours in a simplified artificial medium spiked with 0.05 or 0.5 nM MeHg. Total RNA was extracted using TRI Reagent®. Libraries were prepared with the Illumina TruSeq Stranded mRNA kit and sequenced on an Illumina HiSeq 2500 System.

2016-06-20 | GSE70066 | GEO

Transcriptome of sorted ILC2s in mice fed high-fiber and control diet

Project description:To determine the activation patterns of ILC2s and associated ILC2-intrinsic functional molecules triggered by the high fiber diet, we administered either a control or high fiber diet in WT mice and performed RNA sequencing of FACS-sorted ILC2s from mouse colons. RNAseq libraries were prepared from 1,000 sorted colonic lamina propria ILC2s (CD45+Lin-CD90.2+CD127+KLRG1+) by the Epigenomics Core at WCM using the Clontech SMARTer® Ultra® Low Input RNA Kit V4 (Clontech Laboratories). Libraries were sequenced on an Illumina HiSeq 2500, generating 50 bp single-end reads. Two samples from two control diet-fed WT SPF mice and two samples from two high fiber diet-fed WT SPF mice were used.

2022-08-17 | GSE183443 | GEO

RNA-seq of Aspergillus fumigatus infected to HL-60 derived macrophage-like cells for 0,1, and 2 hours.

Project description:Purpose : The goals of this study are to compare transcriptome profiling (RNA-seq) of Aspergillus fumigatus infected to macrophage-like cells for 0, 1 and 2 hours. Method : HL-60 cells were cultured in RPMI 1640 medium containing 10% fetal bovine serum (FBS) and 1% Gibco™ Antibiotic-Antimycotic at 37°C with 5% CO2. To induce the differentiation of HL-60 cells into macrophage-like cells, HL-60 cells were stimulated with 50 nM 12-o-tetradecanoylphorbol-13-acetate (PMA) for 2 days. A total of 10^3 A.fumigatus conidia were transferred to 5 × 10^4 differentiated HL-60 cells in RPMI 1640 medium supplemented with 5% FBS. After incubating for 0, 1, and 2 hrs, the sample tubes were vigorously agitated with TRIzol® (Invitrogen) containing glass beads to extract total RNA of alive A.fumigatus. ). Libraries were prepared from 2 µg of total RNA using a SMARTer Stranded RNA-Seq Kit (Clontech Laboratories, Inc., USA). Isolation of mRNA was performed using a Poly(A) RNA Selection Kit (LEXOGEN, Inc., Austria). The isolated mRNAs were used for cDNA synthesis and shearing, following the manufacturer’s instructions. Indexing was performed using the Illumina indexes 1-12. An enrichment step was carried out using PCR. Subsequently, libraries were checked using the Agilent 2100 bioanalyzer (DNA High Sensitivity Kit) to evaluate the mean fragment size. Quantification was performed using the library quantification kit with a StepOne Real-Time PCR System (Life Technologies, Inc., USA). High-throughput sequencing was performed as paired-end 100 bp sequencing using a HiSeq 2500 (Illumina, Inc., USA). mRNA-seq reads were mapped using the TopHat software (Cole Trapnell et al., 2009) tool to obtain an alignment file.

2019-08-15 | GSE135818 | GEO

Prolactin-induced protein (PIP) regulates proliferation of luminal A type breast cancer cells in a hormone-independent manner

Project description:RNA was extracted from cells using Aurum Total RNA kit from Bio-Rad Laboratories, Inc., Hercules, CA following the manufacturer’s recommendations. Gene expression profiling was performed using the BeadChip HumanHT-12 v4 Expression kit from Illumina®, which contains 47,231 gene-probes (Illumina® Inc., San Diego, CA). The raw signal intensities were imported and analyzed using the GenomeStudio® data software. After background subtraction and normalization, the signal intensity values were exported to the Partek® genomics expression analysis suite using “Partek's Report Plug-in” option in the GenomeStudio® software. Differentially expressed genes in the dox- versus vehicle-treated samples were identified using the “gene expression” workflow in the Partek® software.

2012-10-29 | GSE41894 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in The White Adipose Tissues of Wild Type (WT) and Adipose-tissue-specific Ces1d knockout (Ces1d FKO) mice

Project description:The goal of this study is to analyze the white adipose tissue transcriptome profiling (RNA-seq) of the wild type and adipose-tissue-specific Ces1d knockout mice. Methods: White adipose tissue mRNA profiles of 14-week-HFD-fed wild-type (WT) and Ces1d adipose tissue knockout mice were collected. Total RNA quality was measured using Agilent RNA 6000 Pico kit (#5067-1513) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). The samples with RNA integrity number (RIN) greater than 7 were used for library preparation. Libraries were prepared with KAPA mRNA HyperPrep (KK8581, Roche) and KAPA UDI Adapter Kit 15μM (KK8727, Roche) following the manufacturer’s instructions. The pooled libraries (n = 10) were paired-end sequenced using 75-cycle High Output Kit v2.5 (#20024907, Illumina, Inc., USA) on Illumina NextSeq 550 System. We used ultrafast universal RNA-seq aligner STAR (v2.5.3a) to conduct the read alignment to mouse reference genome GRCm38. Gene read counts were calculated through setting the argument –quantMode to “GeneCounts” to let STAR count number of uniquely-mapped reads per gene from the GencodeM15 reference. Groups: WT, Sample 1-5; Ces1d FKO, Sample 6-10

2022-03-29 | GSE173893 | GEO

RNA sequencing of primary isolated unstimulated murine splenic cDC from specific pathogen free (SPF), Germ Free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice.

Project description:The transcriptome of primary isolated unstimulated murine splenic cDC from specific pathogen free (SPF) was compared to cDC from Germ Free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice. Cells were isolated and sorted by flow cytometry to high purity. Total RNA was isolated using the RNeasy plus micro kit (Qiagen). Barcoded mRNA seq libraries were prepared from 100 ng of total RNA (RIN>8) using a NEBnext poly(A) mRNA Magnetic Isolation Module and NEBnext UltraII lib prep kit for Illumina (New England Biosciences) according to the manual. Single-end RNA sequencing (59nt) was performed on a HiSeq 2500 (Illumina). Barcoded RNA-seq libraries were onboard clustered using HiSeq® Rapid SR Cluster Kit v2 using 8pM and 59bps were sequenced on the Illumina HiSeq 2500 using HiSeq Rapid SBS Kit v2 (59 Cycle). The raw output data of the HiSeq was preprocessed according to the Illumina standard protocol.

2020-03-30 | E-MTAB-8882 | biostudies-arrayexpress

The effects of mitochondrial- and histone stress on the C. elegans transcriptome

Project description:The aim of this study was to explore whether mitochondrial- and histone stress cause any common changes in global gene expression. For this experiment, we performed RNA sequencing from control RNAi, cco-1 RNAi (mitochondrial stress) and his-3 RNAi (histone stress) treated C. elegans. Nematodes were collected at L4 larval stage, and total RNA was extracted with TriPure Isolation Reagent (Roche). An Illumina Truseq stranded mRNA library was prepared for nine samples (three biological replicates for each sample). Single-end sequencing with 100 cycles was performed by running the nine samples on one lane of an Illumina Hiseq 2500, yielding a minimum of 26 million reads per sample. Although the two stressors were found to have divergent effects on global gene expression, some biological processes such as innate immunity, heat shock response and chromatin remodeler expression are commonly upregulated upon both mitochondrial- and histone stress.

2017-11-28 | GSE105036 | GEO

Mouse gonadal transcriptome at 12.5dpc, 13.5dpc, 16.5dpc and 6dpp.

Project description:we employed RNA-Seq to examine transcriptome profiles of male and female mouse gonads at 12.5dpc, 13.5dpc, 16.5dpc and 6dpp. Methods: Gonadal mRNA profiles of 12.5dpc,13.5dpc, 16.5dpc and 6dpp mice were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500. The cDNA library was constructed with a SMARTer® Ultra Low Input RNA for lllumina® Sequencing kit (Clontech Laboratories) and sequenced on an Illumina HiSeq 2500.After sequencing, clean reads were obtained by removing reads containing the adaptor sequences, reads with > 5% ambiguous bases, and low-quality reads, then mapped to the mouse genome (version: mm10_GRCm38) using TopHat software. Gene expression level was calculated using the fragments per kilobase per million mapped reads method.

2019-10-29 | GSE117590 | GEO

Aurora-A phosphorylates splicing factors and regulates alternative splicing

Project description:The goal of this study is to identify the effect of inhibition of Aurora-A kinase activity on gene expression and RNA splicing. The perturbation of Aurora-A is well known to affect cell cycle distribution. Therefore, we coupled the inhibition of Aurora-A with cell synchronization procedure in order to avoid the indirect effect of cell cycle perturbation on splicing changes. The mRNA -seq libraries were prepared and subjected to paired-end sequencing on Illumina HiSeq 2500 lanes. Differential gene expression and splicing analysis were carried using the edgeR tool and VAST-tools respectively. The RNA seq analysis identified that pharmacological inhibition of Aurora-A affects alternative splicing of 505 genes while having a marginal effect on gene expression. Overall our work identified Aurora-A as a novel splicing kinase and for the first time, describes a broad role of Aurora-A in regulating alternative splicing.

2024-11-21 | GSE160733 | GEO

Circulating Extracellular Vesicular MicroRNA Signatures in Early Gestation Show an Association with Subsequent Clinical Features of Pre-Eclampsia

Project description:We report the differential abundance of cell free miRNAs extracted from extracellular vesicles (EV) in the peripheral blood of pregnant women with or without preeclampsia by Next Generation Sequencing. Maternal blood samples were collected form pregnant women enrolled in the study during first to very early second trimester (11–14 weeks ), mid- to late second trimester (19–22 weeks), third trimester (36 weeks) and at delivery. Extracellular vesicles were isolated from peripheral blood and total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer’s instruction. miRNA libraries were prepared utilizing NEB Next Multiplex small RNA Library prep kit (NEB E7300S; New England Biolabs, Inc, Ipswich, MA, USA) and libraries were subsequently sequenced using the HiSeq-2500 platform with single-end 50bp reads (Illumina Inc.; San Diego, CA, USA).

2024-08-01 | GSE247251 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data