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

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

PROVIDER: PRJNA604024 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10991400_1.fastq.gz	Fastqsanger.gz
	SRR10991400_2.fastq.gz	Fastqsanger.gz
	SRR10991401_1.fastq.gz	Fastqsanger.gz
	SRR10991401_2.fastq.gz	Fastqsanger.gz
	SRR10991402_1.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: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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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.

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

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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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