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Sample GSM3613872 Query DataSets for GSM3613872
Status Public on Feb 10, 2021
Title Sham-R3
Sample type SRA
 
Source name Brain cortex
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: Brain cortex
age: 3 months
Sex: Male
Treatment protocol The mice are treated on day 1, 4, 7, 10, 13, 20, 27 after BCAS surgery
Extracted molecule nuclear RNA
Extraction protocol Cortical tissue was dissected from mice perfused with cold PBS buffer with a transcription inhibitor cocktail at a speed of 6 mL/min for 8 minutes and flash frozen in liquid nitrogen. The frozen tissue was subsequently placed into a tissue dounce for homogenization with homogenization buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH7.8 with freshly added 1mM DTT, 0.15mM spemine (Sigma), 0.5mM spermidine (Sigma), 0.04% BSA (Sigma) and RNase inhibitors (Promega)). 5% IGEPAL (Sigma) stock solution was added to the homogenization buffer to a final concentration of 0.32% for 20 strokes with tight pestle. The homogenate was visually inspected, passed through 40-µm filter (BD Falcon) and layered onto an OptiPrep (Sigma) gradient, as previously described. The gradient was centrifuged at 10,000g for 18 minutes, and nuclei were collected between the 30% and 40% OptiPrep gradient layers. Single nucleic suspension was visually confirmed under microscope and diluted to 80,000 nuclei/mL for nuclei encapsulation and sequencing library preparation following an inDrop protocol as previously described. Approximately about 1,500 nuclei per mouse cortex were encapsulated and passed the quality controls. The prepared libraries are sequenced on Illumina Nova-seq at Broad Institute Walk-up sequencing facility, at a coverage of about 7 billion reads for ~15,000 droplets (~450,000 reads per nuclei).
Sequencing libraries were prepared following an inDrop protocol as previously described (Klein et al, Cell, 2015)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Transcripts were mapped to the mouse transcriptome following an established bioinformatics pipeline (https://github.com/indrops/indrops) for inDrop experiments to create a raw gene-cell counts matrix (Klein et al, Cell, 2015)
The file Unique_barocde_sequences.txt contains the barcode sequenes for each cell ID and is available on the series record.
Genome_build: GRCm38.81
Supplementary_files_format_and_content: text files include Gene_vs_Cell raw counts matrix (single cell matrix)
 
Submission date Feb 20, 2019
Last update date Feb 11, 2021
Contact name Chenxi Qiu
E-mail(s) cqiu@bidmc.harvard.edu
Organization name Harvard Medical School
Street address NRB 858, 77 Avenue Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL24247
Series (1)
GSE126815 Antibody-neutralizable major early driver of Alzheimer’s disease and vascular dementia
Relations
BioSample SAMN10910733
SRA SRX5360233

Supplementary file Size Download File type/resource
GSM3613872_Sham_3.counts.tsv.gz 29.0 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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