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A novel mammalian gene controls mammal-specific neuronal functioning [ChIP-Exo]

ABSTRACT: In mammals brain evolution, specifically that of the cerebellum, is a focus of evolutionary change. Here we functionally characterize the phylogenetically-restricted novel gene, piggyBac transposable element. The ChiP-exonuclease assay protocol was performed as in Serandour's method. The libraries were quantified by using the KAPA library quantification kit for Illumina sequencing platforms (KAPA Biosystems, KK4824) and sequenced on HiSeq following the manufacturer’s protocol.

ORGANISM(S): Homo sapiens

PROVIDER: GSE213758 | GEO | 2022/09/23

REPOSITORIES: GEO

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A novel mammalian gene controls mammal-specific neuronal functioning [RNA-Seq]

Project description:n mammals brain evolution, specifically that of the cerebellum, is a focus of evolutionary change. Here we functionally characterize the phylogenetically-restricted novel gene, piggyBac transposable

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A novel mammalian gene controls mammal-specific neuronal functioning

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Project description:To identify the expression profiles of circRNAs in peripheral blood mononuclear cells (PBMCs) from Ankylosing Spondylitis (AS) patients and healthy controls, we used circRNA sequencing to detect circRNA in 3 samples of PBMCs from AS patients and 3 samples of PBMCs from healthy controls. In brief, total RNA was extracted and purified using Magen Hipure Total RNA Mini Kit (Magen, Guangzhou, China), followed by constructing RNA sequencing libraries with KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems, Inc., MA, USA). After the construction of RNA sequencing libraries, Qubit 3.0 fluorometer (Invitrogen, CA, USA) and the Agilent 2100 bioanalyzer (Applied Biosystems, CA, USA) were used for quality control. Then, the PE150 mode of HiSeq X10 (Illumina Inc., CA, USA) was used for sequencing. Differentially expressed circRNAs were screened with criteria of fold-change>1.5 and p<0.05.

2022-01-05 | GSE178408 | GEO

Glucocorticoid receptor profiling in IMR90, K562 and U2OS (ChIP-exo)

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Simplified ChIP-exo assays

Project description:Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and its ultra-high resolution cousin ChIP-exo are methods that identify where proteins bind along any genome in vivo. ChIP-exo achieves near-base pair resolution by creating exonuclease stop sites just 5’ to where formaldehyde-induced protein-DNA cross-links occur. Whereas construction of ChIP genomic libraries is straightforward and widely adopted for ChIP-seq, ChIP-exo is technically more involved which has resulted in limited adoption. Here we describe multiple ChIP-exo protocols, each with use-specific advantages and limitations. The new versions are greatly simplified through removal of multiple enzymatic steps. This is achieved in part through the use of Tn5 tagmentation and/or single-stranded DNA ligation. The result is greater library yields, lower processing time, and lower cost. A similar streamlined approach was developed for ChIP-seq, called ChIP-seq 1-step, where library construction is achieved in one-step.

2018-08-17 | GSE110681 | GEO

11b3435b-7922-46e1-beea-0faf8d53d116 - samples

Project description:38 PPTCs were sequenced using RNASeq to identify oncogenic variants in driver-unknown tumors and to explore gene expression patterns. RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). Libraries were pooled in equimolar quantities and paired-end sequenced on 2 lanes of a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following IlluminaÃ¢Â€Â™s recommended protocol to generate paired-end reads of 126-bases in length.

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Simplified ChIP-exo assays II

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ChIP-nexus: a novel ChIP-exo protocol for improved detection of in vivo transcription factor binding footprints

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Project description:Multiple companies produce RecJ exonuclease and RNA dependent DNA polymerase for making cDNA. Our standard protocol was developed based on the enzymes from Epicenter (epicenter was recently bought by the Illumina company). As an alternative for the enzymes from EPicenter, we tested the RecJ exonuclease from NEB and Superperscript II from Invitrogen in sRNA library construction using HD adapters [Sorefan et al 2012, Xu et al 2015].

2018-12-20 | GSE102509 | GEO

Characterizing protein-DNA binding event subtypes in ChIP-exo data

Project description:Regulatory proteins associate with the genome either by directly binding cognate DNA motifs or via protein-protein interactions with other regulators. Each genomic recruitment mechanism may be associated with distinct motifs, and may also result in distinct characteristic patterns in high-resolution protein-DNA binding assays. For example, the ChIP-exo protocol precisely characterizes protein-DNA crosslinking patterns by combining chromatin immunoprecipitation (ChIP) with 5’ to 3’ exonuclease digestion. Since different regulatory complexes will result in different protein-DNA crosslinking signatures, analysis of ChIP-exo sequencing tag patterns should enable detection of multiple protein-DNA binding modes for a given regulatory protein. However, current ChIP-exo analysis methods either treat all binding events as being of a uniform type, or rely on the presence of DNA motifs to cluster binding events into subtypes. To systematically detect multiple protein-DNA interaction modes in a single ChIP-exo experiment, we introduce the ChIP-exo mixture model (ChExMix). ChExMix probabilistically models the genomic locations and subtype membership of protein-DNA binding events using both ChIP-exo tag enrichment patterns and DNA sequence information, thus offering a principled and robust approach to characterizing binding subtypes in ChIP-exo data. We demonstrate that ChExMix achieves accurate detection and classification of binding event subtypes using in silico mixed ChIP-exo data. We further demonstrate the unique analysis abilities of ChExMix using a collection of ChIP-exo experiments that profile the binding of key transcription factors in MCF-7 cells. In these data, ChExMix detects cooperative binding interactions between FoxA1, ERalpha, and CTCF, thus demonstrating that ChExMix can effectively stratify ChIP-exo binding events into biologically meaningful subtypes.

2018-02-13 | GSE110502 | GEO

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