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Status |
Public on Jun 30, 2023 |
Title |
snRNA-seq WT |
Sample type |
SRA |
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Source name |
Cortex
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Organism |
Mus musculus |
Characteristics |
tissue: Cortex strain: C57BL/6 genotype: WT
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
Single-nuclei RNA-seq data was processed using mkfastq command from 10X Genomics CellRanger v3.0.1. Assembly: mm10
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Submission date |
Jun 22, 2022 |
Last update date |
Jun 30, 2023 |
Contact name |
Guoping Fan |
E-mail(s) |
guoping.fan@gmail.com
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Organization name |
university of california, los angeles
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Department |
Human Genetics
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Street address |
695 Charles E Young Drive South
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City |
los angeles |
State/province |
ca |
ZIP/Postal code |
90095 |
Country |
USA |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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