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Status |
Public on May 27, 2021 |
Title |
WT_1 |
Sample type |
SRA |
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Source name |
hippocampus
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Organism |
Mus musculus |
Characteristics |
tissue: hippocampus age: 7 month genotype: wild type strain: C57BL/6
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Extracted molecule |
total RNA |
Extraction protocol |
Single nuclei were isolated based on the published protocol with modifications of Krishnaswami et al., 2016. After dissection, hippocampi were homogenized in a cold Dounce homogenizer after dissection. The homogenate was centrifuged at 1,000g for 8 min at 4 °C to pellet nuclei. Nuclei were resuspended in 1 ml 29% iodixanol buffer and centrifuged at 13,500 g for 20 min at 4°C. Supernatant and floating myelin were removed after centrifugation. Nuclei were resuspended in 100 µl nuclei storage buffer and filtered using a 40 µm cell strainer. Nuclei were stained with trypan blue to and counted using a hemocytometer. RNA libraries were prepared for sequencing using standard 10X Genomics protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
Sample demultiplexing, barcode processing and single-cell counting was performed using the Cell Ranger Single-Cell Software Suite (10x Genomics, version 3.0.2). Cellranger count was used to align samples to the reference genome (mm10). The counting matrix were imported into Seurat package (version 3.0) in R (version 3.6.2) for subsequent analysis. Genome_build: mm10
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Submission date |
Sep 15, 2020 |
Last update date |
May 27, 2021 |
Contact name |
Peng Xu |
E-mail(s) |
pxu@mail.rockefeller.edu
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Organization name |
The Rockefeller University
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Lab |
Greengard lab
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Street address |
1230 York Avenue
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City |
New York |
State/province |
NY |
ZIP/Postal code |
10065 |
Country |
USA |
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Platform ID |
GPL24247 |
Series (1) |
GSE157985 |
GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer’s disease |
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Relations |
BioSample |
SAMN16140310 |
SRA |
SRX9125392 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4783646_GSAP_WT1_08212019_barcodes.tsv.gz |
28.7 Kb |
(ftp)(http) |
TSV |
GSM4783646_GSAP_WT1_08212019_features.tsv.gz |
265.9 Kb |
(ftp)(http) |
TSV |
GSM4783646_GSAP_WT1_08212019_matrix.mtx.gz |
57.7 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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