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Status |
Public on Jun 23, 2022 |
Title |
Control-5-MAP2 |
Sample type |
SRA |
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Source name |
Brain, prefrontal cortex, Brodmann area 9 (BA9); Postmortem, fresh frozen
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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
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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.
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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 |
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.
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Submission date |
Jun 22, 2022 |
Last update date |
Nov 29, 2022 |
Contact name |
Inma Cobos |
E-mail(s) |
icobos@stanford.edu
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Phone |
6507258200
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Organization name |
STANFORD UNIVERSITY MEDICAL SCHOOL
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Street address |
300 Pasteur Drive, Lane Building, L235
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City |
Stanford |
State/province |
California |
ZIP/Postal code |
94305-5324 |
Country |
USA |
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Platform ID |
GPL24676 |
Series (1) |
GSE129308 |
Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer’s disease |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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