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Sample GSM6528212 Query DataSets for GSM6528212
Status Public on Sep 04, 2022
Title Bulk RNA-seq E4_Old_Bulk RNA-seq rep1
Sample type SRA
 
Source name Brain
Organism Mus musculus
Characteristics tissue: Brain
cell type: Brain cells
genotype: ApoE4
treatment: Old_aged
Extracted molecule total RNA
Extraction protocol The mirroring hemisphere (right) from brains processed for scRNAseq were immediately placed in OCT compound (Fisher HealthCare Tissue Plus O.C.T. Compound Clear 4585) and gently lowered into isopentane (Sigma Aldrich 2-Methylbutane M32631) in a beaker surrounded by dry ice (isopentane chilled to approximately -70°C). Brains were submerged for 60 seconds, placed on dry ice, wrapped in aluminum foil, and stored at -80°C until sectioning. Prepared brain hemispheres were cryosectioned to 10 μm thick coronal sections at approximately Bregma -2.00 mm. Serial 10 μm sections immediately rostral and caudal to the section mounted on the Visium Spatial Gene Expression slide (10X Genomics) were collected for immunohistochemistry. Optimal tissue permeabilization time was determined using the manufacturer’s optimization protocols (10X Genomics, Visium Spatial Tissue Optimization), and accordingly, experimental tissues were permeabilized for 18 min for Visium Spatial Gene Expression analysis. Prior to library preparation, tissue sections were methanol-fixed, stained with hematoxylin and eosin (H&E), and imaged on a Nikon NiU microscope with Fi3 color camera. Sections were then permeabilized and processed to obtain cDNA libraries, which were subsequently prepared according to the manufacturer’s protocol (https://support.10xgenomics.com/spatial-gene-expression/libraryprep).
Sample libraries were constructed using Next GEM automated 3’ reagents (10X Genomics, v3.1) following manufacturer’s suggested protocol (#CG000286 Rev B). Final library quantification and quality check was performed using BioAnalyzer (Agilent), and sequencing performed on a NovaSeq 6000 S4 flow cell, 150 bp Paired-End sequencing (Novogene).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description bulk_seq
Data processing Raw FASTQ data and H&E images were processed by the Space Ranger v1.3.0 (10X Genomics) pipeline. Illumina base call (BCL) files from the sequencing instrument were converted to FASTQ format for each sample using the mkfastq. Visium spatial expression libraries were analyzed with the count command. Image alignment to predefined spots was performed by the fiducial alignment grid of the tissue image to determine the orientation and position of the input image. Sequencing reads were aligned to the mm10 reference genome using STAR (v2.5.1b) aligner. Gene expression profiling in each spot was performed with UMI and 10X barcode information.
Assembly: mm10
Supplementary files format and content: Count txt files
 
Submission date Aug 30, 2022
Last update date Sep 15, 2022
Contact name Lance A Johnson
E-mail(s) johnson.lancea@gmail.com
Phone 8593232746
Organization name University of Kentucky
Department Physiology/Sanders-Brown Center on Aging
Street address 760 Press Ave, HKRB 135
City Lexington
State/province KY
ZIP/Postal code 40536
Country USA
 
Platform ID GPL24247
Series (2)
GSE212343 APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge [Bulk RNA-seq]
GSE213391 APOE modulates microglial immunometabolism in response to age, amyloid pathology, and inflammatory challenge
Relations
BioSample SAMN30597699
SRA SRX17356401

Supplementary file Size Download File type/resource
GSM6528212_C3_counts.txt.gz 134.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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