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| Scope: Self Platform Samples Series Family Format: HTML SOFT MINiML Amount: Brief Quick GEO accession: |  |
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| Sample GSM4214753 | Query DataSets for GSM4214753 |
| | Status | Public on Jan 30, 2020 | | Title | Spiny projection neurons, NonCar_Nme1OX, rep4 | | Sample type | SRA | | Source name | Striatum | | Organism | Mus musculus | | Characteristics | disease state: R62 mouse model of HDtissue: Striatumcell type: spiny projection neuronsvirus: Nme1OXgenotype: NonCar | | 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: GRCm38Supplementary_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 | | E-mail(s) | [email protected] | | 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 |
| | Relations | | BioSample | SAMN13541974 | | SRA | SRX7348182 |
| Supplementary file | Size | Download | File type/resource | | GSM4214753_MW_NME1_9_processed_data_files.tar.gz | 35.8 Mb | (ftp)(http) | TAR | SRA Run Selector | | Raw data are available in SRA | | Processed data provided as supplementary file |
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