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Sample GSM3704375 Query DataSets for GSM3704375
Status Public on Aug 05, 2020
Title 6b-All_Nuclei
Sample type SRA
 
Source name Brain, prefrontal cortex, Brodmann area 9 (BA9); Postmortem, fresh frozen
Organism Homo sapiens
Characteristics tissue: brain
number of cells sequenced: 3,555
age: 73
gender: F
pmi (hr): 13
rin: 5.7
brain weight (gr): 1,300
brain region: Brodmann area 9 (BA9)
disease: Alzheimer's disease
ad stage: NIH-AA score A3B3C3; Braak VI
other pathology: none
Biomaterial provider UCLA-Easton Center brain bank; Departments of Neurology and Pathology; UCLA David Geffen School of Medicine
Extracted molecule polyA RNA
Extraction protocol Comparison of single transcriptomes from neuronal nuclei versus somas, isolated using the pan-neuronal markers NeuN (nuclear) and MAP2 (cytoplasmic): Tissue from the prefrontal cortex (Brodmann area 9; BA9) of an AD Braak stage VI patient (case # 6) was thawed on ice, and the cortical ribbon spanning all cortical layers was micro-dissected. Dissociation of individual nuclei used mechanical force and a detergent (0.1% triton); dissociation of individual somas used gentle mechanical force. Immunostaining and FACS using the pan-neuronal markers NeuN or MAP2 was used to collect three populations: MAP2+, NeuN+, and All nuclei (NeuN+ and NeuN-). RNA capture and library preparation was performed using the 10× Genomics Chromium Single Cell 3’ v2 assay. The generated paired-end libraries were sequenced on Illumina Novaseq 6000.
Single-cell RNA capture and library preparation was performed using the 10× Genomics Chromium Single Cell 3’ v2 assay according to the manufacturer’s user manual. The numbers of cells loaded ranged from 1,400–11,000 to capture the maximum number of cells up to an upper limit of ~5,000 cells per sample (for an expected cell capture efficiency of ~40%). For cDNA amplification, the number of PCR cycles was 13–15 (adjusted to the targeted cell recovery). For library construction, the number of cycles for the sample index PCR reaction was 12–13 (adjusted to the quantified cDNA input). The generated paired-end libraries were sequenced on an Illumina Novaseq 6000 (2 × 100); 26 bp for read 1 (cell barcode and UMI), 8 bps for the i7 index, and 98 bps for read 2.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description polyA mRNA (nuclear)
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.
Genome_build: GRCh38 1.2.0 (10x Cellranger)
Supplementary_files_format_and_content: Matrices in the Hierarchical Data Format (HDF5 or H5). Obtained with Cellranger v3.0.1; cellranger count function, default parameters.
 
Submission date Apr 03, 2019
Last update date Aug 05, 2020
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 SAMN11334684
SRA SRX5635330

Supplementary file Size Download File type/resource
GSM3704375_6b-All_filtered_feature_bc_matrix.h5 6.2 Mb (ftp)(http) H5
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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