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Optimized ATAC-seq library preparation from Drosophila neurons

ABSTRACT: Optimized ATAC-seq library preparation from Drosophila neurons

PROVIDER: PRJNA812007 | ENA |

REPOSITORIES: ENA

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Optimized ATAC-seq library preparation from Drosophila neurons

Project description:We optimzed ATAC-seq library preparation for use with Drosophila melanogaster. The protocol addresses factors specific to fruit flies, such as the insect exoskeleton and smaller genome size. The optimized protocol provides guidelines for sample input, nuclei isolation, and enzymatic reaction times. The data included here were generated using our optimized library preparation workflow.

2022-04-20 | GSE197760 | GEO

Library preparation Pool-seq

Project description:Evaluating different library preparation methods for Pool-seq

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Evaluation of three small RNA library preparation kits on serum-derived RNA

Project description:We evaluated the effect of the small RNA library preparation method on 5' tRNA-halves and miRNA abundance in libraries prepared from serum RNA using three commercially available small RNA library preparation kits (TruSeq small RNA library preparation kit v2 (Illumina), TailorMix miRNA sample preparation kit v2 (Seqmatic) and the NEBNext Multiplex Small RNA library prep kit (New England Biolabs)). RNA isolated from 100 µl of serum collected from healthy mice was used as input for the preparation of a small RNA library in duplicate and libraries were single end sequenced.

2017-02-22 | GSE88914 | GEO

Comparison of library preparation methods

Project description:Comparison of library preparation methods using Cryptococcus neoformans var. grubii

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Open chromatin profiling (ATAC-seq) of SGBS human preadipocytes (days 0, 2, 8 and 16 of differentiation to adipocytes) and iPSC-derived hypothalamic neurons (days 12, 16 and 27 of differentiation)

Project description:Human SGBS preadipocytes were differentiated into adipocytes, and human iPSCs were differentiated into hypothalamic neurons. Cells were collected for ATAC-seq at several differentiation stages. The differentiations were performed in one biological replicate, with two technical replicates (different wells of the differentiation that were also processed individually during library preparation). SGBS Day0: Represents the preadipocyte state. SGBS Day2: Represents immature adipocytes. SGBS Day8: Represents early mature adipocytes. SGBS Day16: Represents mature adipocytes. Hypothalamic Day 12: Represents early hypothalamic neurons. Hypothalamic Day 16: Represents mid hypothalamic neurons. Hypothalamic Day 27: Represents mature hypothalamic neurons.

2021-05-22 | E-MTAB-10462 | biostudies-arrayexpress

Immunoglobulin library preparation for NGS

Project description:High-quality immunoglobulin library preparation for germline inference and repertoire expression analysis.

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Immunoglobulin library preparation for NGS

Project description:High-quality immunoglobulin library preparation for germline inference and repertoire expression analysis.

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Splinted Ligation Adapter Tagging, a novel library preparation for whole genome bisulphite sequencing

Project description:Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.

2016-10-27 | GSE89213 | GEO

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

Project description: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.

2022-03-04 | GSE195752 | GEO

ATAC-seq of mESCs differentiation into neurons

Project description:Mouse WT129 ESCs were differentiated into glutamatergic neurons and samples were collected at days 0 (mESCs), 4 (embryoid bodies), 8 (neuronal precursors) and 12 (neurons). ATAC-seq experiment in 4 biological replicates was performed at 4 indicated above time points to profile chromatin structure changes during differentiation.

2020-05-20 | E-MTAB-8194 | biostudies-arrayexpress

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