Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole genome DNA methylation profiling of D2 medium spiny neurons in mouse nucleus accumbens using two independent library preparation methods

ABSTRACT: We isolated genomic DNA from adult male mouse nucleus accumbens (NAc) D2 medium spiny neurons (D2-MSN) by fluorescence-activated cell sorting. We performed the whole genome methylation profiling using two independent library preparation methods, namely the sodium bisulfite-based Accel-NGS Methyl-Seq (AM-seq) of Swift biosciences and the enzymatic conversion-based method Enzymatic Methyl-seq (EM-seq) from New England Biolabs, on two identical samples. We mapped about 400 million paired-end reads to the mouse genome (build mm10) and assessed measures of each methylome by two methods. This study provided a side-by-side comparison of two independent whole genome profiling methods for low-input neuronal samples.

ORGANISM(S): Mus musculus

PROVIDER: GSE195752 | GEO | 2022/03/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome-wide gene expression patterns in reprogramming MEF infected by SeVdp vectors carrying KLF4 WT or L507A mutant

Project description:To evaluate global gene expression pattern changes between KLF4 L507A and WT during reprogramming, RNA-Seq was performed on the samples collected from reprogramming MEF infected with SeVdp vectors carrying KLF4 WT or L507A mutant. Original MEF and resulting miPSCs (mouse iPSCs) were also used as samples. RNA-seq library was generated using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) and NEBNext rRNA Delepletion Kit (New England Biolabs) by Lab Droid “Maholo” (Robotic Biology Institute) automatically. Paired-end sequencing of the libraries was performed using Novaseq 6000 SP Sequencing system using SP 100 cycle kit (Illumina). Reads from RNA-seq experiments were mapped to the mouse genome (GRCm38 or mm10) and analyzed for differential gene expression and PCA (principal component analysis) using CLC Genomics Workbench (Qiagen) software.

2021-09-27 | GSE184449 | GEO

Integrative Epigenetic Analysis Reveals Therapeutic Targets to the DNA Methyltransferase Inhibitor SGI-110 in Hepatocellular Carcinoma Cells [methylation]

Project description:For the AcceSssIble assay, nuclei preparation and M.SssI methyltransferase (New England BioLabs) treatment were performed. The subsequent Infinium DNA methylation assay was performed at the University of Southern California Molecular Genomics Core Facility according to the manufacturer’s specifications (Illumina).

2018-06-26 | GSE105066 | GEO

Small RNA sequencing of mouse bone marrow derived extracellular vesicles [EV.sRNA]

Project description:Mouse BM extracellular vesicles were isolated from Ocn-GFP Topaz mice using the Exoeasy and miRneasy (Qiagen). Small RNA libraries were constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England biolabs). Libraries were sequenced using Hiseq2500 instrument

2021-12-08 | GSE127864 | GEO

mRNA-seq of H3.3 mutant (K9A; K27A; K79A) and control mESCs

Project description:Mouse embryonic stem cells (i.e., mESCs; line ESC 129-B13) were genetically modified using CRISPR-Cas9 to mutate the H3f3b locus, in order to carry homozygous lysine-to-alanine substitution of residues K9, K27 or K79. Two control mESC lines carrying knock-out of the H3f3a gene were used as background for the editing. To compare the transcriptional profiles of the H3.3 mutant and control mESC lines, three independent replicates per condition were grown and RNA was extracted. After quality assessment of the RNA, messenger RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs) and sequencing libraries were prepared using the NEBNext Ultra II RNA Library Preparation Kit for Illumina (New England BioLabs). Sequencing was performed on a NextSeq500 platform in single-end mode (75bp reads).

2024-03-09 | E-MTAB-12866 | biostudies-arrayexpress

Project description:Enzymatic Methyl-Seq of Chionographis japonica

| PRJEB58127 | ENA

Analysis of CAL165 cells transcriptome using RNASeq

Project description:Total RNA extracted from the head and neck cell line CAL165 were purified using miRNeasy minikit (Qiagen). RNA libraries were then generated with the NEB next small library prep set for SOLID (New England Biolabs) and sequenced on the Applied Biosystems SOLiD 5500 wildfire system following the manufacturer's instructions.

2017-06-07 | GSE89510 | GEO

Analysis by RNAseq of the transcriptome of different stage of skin carcinogenesis induced by topical application of DMBA/TPA

Project description:Total RNA extracted from biopsies of healthy skin, papilloma, SCC Tumor and of 2 cell lines isolated from these tumors were purified using miRNeasy minikit (Qiagen). RNA libraries were then generated with the NEB next small library prep set for SOLID (New England Biolabs) and sequenced on the Applied Biosystems SOLiD 5500 wildfire system following the manufacturer's instructions.

2017-06-07 | GSE89509 | GEO

RNA-seq of Arabidopsis thaliana siliques from WT and MYB73 overexpression lines

Project description:This experiment seeks to elucidate the functional role of MYB73 in Arabidopsis thaliana siliques via differential gene expression (DGE) analysis. Total RNA were extracted from pooled Arabidopsis siliques at 12 days after flowering (DAF) for 3 biological replicates from WT and MYB73-OE lines. RNA-seq libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) for Illumina according to the manufacturer’s instruction and sequenced with Novaseq-6000 (Illumina) using paired-end sequencing with read lengths of 150 base pairs at sequencing depths of ~ 2 million reads per sample.

2024-11-01 | E-MTAB-14541 | biostudies-arrayexpress

Project description:Target-enriched enzymatic methyl sequencing

| PRJNA861281 | ENA

Cross-Site Comparison of Ribosomal Depletion Kits for Illumina RNAseq Library Construction

Project description:In a cross-site study we evaluated the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. We found that all of the kits were capable of performing significant ribosomal depletion, though there were differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes among kits suggested that transcript length may be a key factor in library production efficiency. These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them.

2018-02-01 | GSE100127 | 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