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| Scope: Self Platform Samples Series Family Format: HTML SOFT MINiML Amount: Brief Quick GEO accession: |  |
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| Sample GSM4601694 | Query DataSets for GSM4601694 |
| | Status | Public on Jul 17, 2020 | | Title | 190807_zQ175_snRNA-B10 | | Sample type | SRA | | Source name | Striatum | | Organism | Mus musculus | | Characteristics | tissue: Striatumgenotype: zQ175+tissue id: NA | | 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 NextSeq 500 | | Data processing | Basecalls converted to FASTQ with Cellranger v3.1.FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.Genome build: GRCm38/mm10Supplementary_files_format_and_content: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.snRNA-seq: Basecalls converted to FASTQ with Cellranger v3.1.snRNA-seq: FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.Genome_build: snRNA-seq: GRCm38/mm10Supplementary_files_format_and_content: snRNA-seq: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.TRAP: FASTQs files were aligned to the Mus musculus genome using STAR v2.4.2a. Read counts were generated by STAR using the --quantMode GeneCounts option, along with the default options, except for --outFilterMismatchNoverLmax, which was set to 0.04 (from 0.3), --outFilterMismatchNmax, which was set at 999 (from 10), --alignIntronMax, which was set to 1000000, and --alignMatesGapMax, which was set to 1000000.Retro-TRAP: FASTQs files of 50-bp single-end sequencing reads were aligned using STAR 2.4 RNA-Seq aligner. As note, technical replicate data were merged for alignment. The mapped reads were processed with HTSeq to generate gene counts (GENCODE.vM9 version of mouse gene annotation).Genome_build: TRAP: GRCm38.78, Retro-TRAP: GRCm38.p4Supplementary_files_format_and_content: TRAP: TSV and TXT files containing raw counts and reads per kilobase mission of each gene per sample. | | Submission date | Jun 08, 2020 | | Last update date | Jul 18, 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 | GPL19057 | | Series (1) | | GSE152058 | Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation |
| | Relations | | BioSample | SAMN15181354 | | SRA | SRX8503736 |
| Supplementary file | Size | Download | File type/resource | | GSM4601694_190807_zQ175_snRNA-B10_matrix.mtx.gz | 129.1 Mb | (ftp)(http) | MTX | SRA Run Selector | | Raw data are available in SRA | | Processed data provided as supplementary file |
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