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Sample GSM6261348 Query DataSets for GSM6261348
Status Public on Jun 23, 2022
Title Control-5-MAP2
Sample type SRA
 
Source name Brain, prefrontal cortex, Brodmann area 9 (BA9); Postmortem, fresh frozen
Organism Homo sapiens
Characteristics tissue: Brain, prefrontal cortex, Brodmann area 9 (BA9); Postmortem, fresh frozen
number of cells sequenced: 8,140
age: 72
gender: M
pmi (hr): 16.4
rin: 6.4
brain weight (gr): N/A
disease: Healthy control
ad stage: NIH-AA score A0B1C0
other pathology: none
biomaterial provider: NIH NeuroBioBank - Mount Sinai Brain Bank
Extracted molecule polyA RNA
Extraction protocol Fresh-frozen tissue from the prefrontal cortex (Brodmann area 9; BA9) of healthy control donors was thawed on ice, and the cortical ribbon spanning all cortical layers was micro-dissected. Gentle mechanical dissociation without detergents or enzymatic digestion followed by sucrose-iodixanol gradient centrifugation was used to purify cells with relatively well-preserved somas. Immunostaining and fluorescence-activated cell sorting using the pan-neuronal marker MAP2 was used to collect neuronal somas.
RNA capture and library preparation was performed using the 10× Genomics Chromium Single Cell 3’ v2 or v3 assay.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Sequencing data quality check. Performed with Illumina SAV.
Demultiplexing. Performed with Illumina Bcl2fastq2 v 2.19 program.
Alignment and filtering. Performed with Cellranger v3.0.1; cellranger count function, default parameters.
Barcode and UMI counting. Performed with Cellranger v3.0.1; cellranger count function, default parameters.
Assembly: GRCh38 1.2.0 (10x Cellranger)
Supplementary files format and content: Matrices in the Hierarchical Data Format (HDF5 or H5) from Cellranger v3.0.1; cellranger count function, default parameters.
 
Submission date Jun 22, 2022
Last update date Nov 29, 2022
Contact name Inma Cobos
E-mail(s) icobos@stanford.edu
Phone 6507258200
Organization name STANFORD UNIVERSITY MEDICAL SCHOOL
Street address 300 Pasteur Drive, Lane Building, L235
City Stanford
State/province California
ZIP/Postal code 94305-5324
Country USA
 
Platform ID GPL24676
Series (1)
GSE129308 Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer’s disease
Relations
BioSample SAMN29251752
SRA SRX15830708

Supplementary file Size Download File type/resource
GSM6261348_Control-5-MAP2_filtered_feature_bc_matrix.h5 16.9 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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