 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
| E-mail(s) |
mheiman@mit.edu
|
| 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 |
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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
