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Sample GSM4214763 Query DataSets for GSM4214763
Status Public on Jan 30, 2020
Title Spiny projection neurons, R62Hemi_Nme1OX, rep4
Sample type SRA
Source name Striatum
Organism Mus musculus
Characteristics disease state: R62 mouse model of HD
tissue: Striatum
cell type: spiny projection neurons
virus: Nme1OX
genotype: R62Hemi
Extracted molecule total RNA
Extraction protocol Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol. The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA.
Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description snRNA
Data processing Basecalls converted to FASTQ with Cellranger v3.1.
FASTQ aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCm38 reference that included EGFP.
Genome_build: GRCm38
Supplementary_files_format_and_content: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.
Submission date Dec 11, 2019
Last update date Feb 01, 2020
Contact name Myriam Heiman
Organization name Massachusetts Institute of Technology
Department Brain and Cognitive Sciences
Lab Heiman
Street address 77 Massachusetts Ave., Bldg 46-4285
City Cambridge
State/province Massachusetts
ZIP/Postal code 02139
Country USA
Platform ID GPL24247
Series (1)
GSE141856 Genome-wide in vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity
BioSample SAMN13541960
SRA SRX7348192

Supplementary file Size Download File type/resource
GSM4214763_MW_NME1_19_processed_data_files.tar.gz 42.1 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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