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Sample GSM4783646 Query DataSets for GSM4783646
Status Public on May 27, 2021
Title WT_1
Sample type SRA
 
Source name hippocampus
Organism Mus musculus
Characteristics tissue: hippocampus
age: 7 month
genotype: wild type
strain: C57BL/6
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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
 
Submission date Sep 15, 2020
Last update date May 27, 2021
Contact name Peng Xu
E-mail(s) pxu@mail.rockefeller.edu
Organization name The Rockefeller University
Lab Greengard lab
Street address 1230 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL24247
Series (1)
GSE157985 GSAP regulates mitochondrial function through Mitochondria-associated ER membrane in the pathogenesis of Alzheimer’s disease
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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