For treatment of neurons, mouse α-synuclein PFFs, which were generated at a concentration of 5 mg/mL were vortexed and diluted with Dulbecco’s phosphate-buffered saline (DPBS, Corning Cat#21–031-CV) to 100 μg/mL. They were then sonicated on high for 10 cycles of 30 seconds on, 30 seconds off (Diagenode Biorupter UCD-300 bath sonicator). α-Synuclein PFFs were then diluted in neuron media to 5 μg/mL and added to neuron cultures at the noted concentrations.
Biorupter ucd 300
Manufactured by Diagenode
The Biorupter UCD-300 is a high-performance ultrasonic cell disruptor designed for efficient sample preparation. It utilizes ultrasonic waves to disrupt cells, tissues, and other biological samples, allowing for the release of intracellular contents such as proteins, nucleic acids, and organelles. The Biorupter UCD-300 is a versatile and powerful tool suitable for a wide range of applications in life science research and molecular biology.
Automatically generated - may contain errors
Lab products found in correlation
Dulbecco phosphate buffered saline (dpbs), by Corning (1 mentions)
Hiseq 2000 platform, by Illumina (1 mentions)
Magnify chromatin immunoprecipitation system, by Thermo Fisher Scientific (1 mentions)
Anti myod, by Santa Cruz Biotechnology (1 mentions)
Anti h3k4me2, by Abcam (1 mentions)
Casava pipeline, by Illumina (1 mentions)
Nextflex chip seq kit, by Bio Scientific (1 mentions)
Anti h3k4me3, by Abcam (1 mentions)
2 protocols using biorupter ucd 300
1
Preparing Mouse α-Synuclein PFFs for Neuron Treatment
2
ChIP-seq Protocol with Modifications
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ChIP was performed as described before [29 (link)]. Briefly, the MAGnify™ Chromatin Immunoprecipitation System (Life Technologies, 49–2024) was used with some modifications. Sonication was performed using the Biorupter UCD300 (Diagenode) to obtain chromatin fragments of approximately 100–300 bp. The following antibodies were used for ChIP: anti-H3K4me2 (Abcam ab7766), anti-H3K4me3 (Abcam ab8580), and anti-MyoD (Santa Cruz, sc-760). Sequencing libraries were prepared using the NEXTflex™ ChIP-Seq Kit (Bio Scientific, 5143) according to an in-house modified protocol. The libraries were 51 bp single-end sequenced on an Illumina HiSeq 2000 platform. Base calling was performed with the Illumina Casava pipeline version 1.8.0. Initial sequencing quality assessment was based on data passing the Illumina Chastity filter. The raw and processed ChIP-seq data was submitted to GEO (GSE63716).
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