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Sample GSM6260249 Query DataSets for GSM6260249
Status Public on Jun 30, 2023
Title snRNA-seq WT
Sample type SRA
 
Source name Cortex
Organism Mus musculus
Characteristics tissue: Cortex
strain: C57BL/6
genotype: WT
Extracted molecule total RNA
Extraction protocol Surgically resected cortical tissue was homogenized using a glass dounce homogenizer in 2 ml of ice-cold Nuclei EZ lysis buffer (#EZ PREP NUC-101, Sigma) and was incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C, washed with 4 ml ice-cold Nuclei EZ lysis buffer and, incubated on ice for 5 min. Nuclei were centrifuged at 500 × g for 5 min at 4 °C. After centrifugation, the nuclei were resuspended in 1 ml of nuclei suspension buffer (NSB) consisting of 1XPBS, 1%BSA (#AM2618, Thermo Fisher Scientific) and 0.2U/ul RNAse inhibitor (#AM2694, Thermo Fisher Scientific) and were filtered through a 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art). Nuclei concentration was determined using 0.4% Trypan Blue (#15250061, Thermo Fisher Scientific). Final concentration of 1000 nuclei/μl was adjusted with NSB.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v2 according to the manufacturer’s protocol. 
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Single-nuclei RNA-seq data was processed using mkfastq command from 10X Genomics CellRanger v3.0.1.
Assembly: mm10
 
Submission date Jun 22, 2022
Last update date Jun 30, 2023
Contact name Guoping Fan
E-mail(s) guoping.fan@gmail.com
Organization name university of california, los angeles
Department Human Genetics
Street address 695 Charles E Young Drive South
City los angeles
State/province ca
ZIP/Postal code 90095
Country USA
 
Platform ID GPL21103
Series (2)
GSE206664 Reversing lysosome-mTORC1-ribosome axis dysregulations to mitigate C9FTD/ALS neurodegeneration [snRNA-Seq]
GSE206666 Reversing lysosome-mTORC1-ribosome axis dysregulations to mitigate C9FTD/ALS neurodegeneration
Relations
BioSample SAMN29248525
SRA SRX15826652

Supplementary file Size Download File type/resource
GSM6260249_wt_ana.tar.gz 61.3 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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