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ATAC-Seq for control and huntington's disease iPSC-derived medium spiny neuron-like cells

ABSTRACT: ATAC-Seq for control and huntington's disease iPSC-derived medium spiny neuron-like cells

PROVIDER: PRJNA603902 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10988638.fastq.gz	Fastqsanger.gz
	SRR10988639.fastq.gz	Fastqsanger.gz
	SRR10988640.fastq.gz	Fastqsanger.gz
	SRR10988641.fastq.gz	Fastqsanger.gz
	SRR10988642.fastq.gz	Fastqsanger.gz

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Total RNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells

Project description:Total RNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells

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ATAC-Seq for control and huntington's disease iPSC-derived medium spiny neuron-like cells

Project description:HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron-like cells. Three control in triplicate, one control in duplicate, one HD samples with CAG repeat length in typical adult onset range in triplicate and one in duplicate, and five HD samples with CAG repeat length in typical juvenile onset range in triplicate were differentiated as biological growth replicate (separate differentiations) into medium spiny neuron-like cells. Total RNA was isolated using the Qiagen RNeasy Kit and QIAshredders for cell lysis. 1 µg of RNA with RIN values >9 were used for library preparation using the strand specific Illumina TruSeq Total RNA protocol. Libraries were sequenced on the HiSeq 2500 using 100 cycles to obtain paired-end 100 reads at >50M reads per sample.

2020-03-01 | GSE144518 | GEO

Single cell RNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells

Project description:Single cell RNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells

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H3K4me3 ChIP-Seq profiles of control and huntington's disease iPSC-derived medium spiny neuron-like cells

Project description:H3K4me3 ChIP-Seq profiles of control and huntington's disease iPSC-derived medium spiny neuron-like cells

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Total RNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells

Project description:HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron (MSN)-like cells. Three control in triplicate, one control in duplicate, one HD samples with CAG repeat length in typical adult onset range in triplicate and one in duplicate, and five HD samples with CAG repeat length in typical juvenile onset range in triplicate were differentiated as biological growth replicate (separate differentiations) into medium spiny neuron-like cells. Total RNA was isolated using the Qiagen RNeasy Kit and QIAshredders for cell lysis. 1 µg of RNA with RIN values >9 were used for library preparation using the strand specific Illumina TruSeq Total RNA protocol. Libraries were sequenced on the HiSeq 2500 using 100 cycles to obtain paired-end 100 reads at >50M reads per sample.

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H3K4me3 ChIP-Seq profiles of control and huntington's disease iPSC-derived medium spiny neuron-like cells

2020-03-01 | GSE144493 | GEO

Single cell RNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells

Project description:HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron-like cells. One control and one HD sample with CAG repeat length in typical adult onset range were differentiated into medium spiny neuron-like cells. Cells were dissociated into single cell suspension and single cell viability for each sample was determined (86.9% for control, 80.9% for HD). Cells were processed using 10x genomics single cell platform. Libraries were sequenced on the HiSeq 4000 using 100 cycles to obtain paired-end 100 reads at >50M reads per cell. The estimated number of cells sampled was 5,070 (control) and 3,829 (HD) with an average number of reads per cell at 31,675 (control) and 41,939 (HDQ). After QC filtering, the data were aggregated using Cell Ranger and gene-by-cell expression matrices generated and used as input for Seurat and Scanpy.

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Expression data from of HD-iPSC and CON-iPSC neuron derivatives

Project description:Compared the global gene expression profiles of HD- and CON-iPSC-derived neurons We used microarrays to detail the global programme of gene expression for comparing the global gene expression profiles of HD- and CON-iPSC-derived neurons and facilitating studies of medium spiny neurons (MSN)-degenerative processes of Huntington's Disease (HD).

2015-09-02 | GSE59051 | GEO

Transcriptomic Characterization Reveals Disrupted Medium Spiny Neuron Trajectories in Huntington's Disease and Possible Therapeutic Avenues

Project description:Transcriptomic Characterization Reveals Disrupted Medium Spiny Neuron Trajectories in Huntington's Disease and Possible Therapeutic Avenues

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mRNA Sequencing of control and huntington's disease iPSC-derived medium spiny neuron-like cells and Q175 HET or WT mice. Plus and minus knockdown of PIAS1.

Project description:HD and control patient-derived induced pluripotent stem cells were used to generate medium spiny neuron-like cells. four control in duplicate and three HD samples in duplicate with CAG repeat length in juvenile onset range were differentiated as biological growth replicates (separate differentiations) into medium spiny neuron-like cells. Cells were treated with LNPs with siRNA for knockdown of PIAS1 or a luciferase control. Total RNA was isolated using the Qiagen RNeasy Kit and QIAshredders for cell lysis. For mouse data WT and HET GFP+ micro-dissected flash frozen brain regions (striatum) were homogenized in TRIzol reagent (Invitrogen) and RNA were collected and purified using RNEasy Mini kit (Qiagen). Mice were treated with AAV2/1 expressing either a miRNA against Pias1 (miPias1.3), a control scrambled miRNA (miSafe). 1 µg of RNA with RIN values >8 were used for library preparation using the strand specific Illumina TruSeq mRNA protocol. Libraries were sequenced on the HiSeq 4000 using 100 cycles to obtain paired-end 100 reads.

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