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Status |
Public on Sep 04, 2022 |
Title |
Bulk RNA-seq E4_Old_Bulk RNA-seq rep1 |
Sample type |
SRA |
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Source name |
Brain
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Organism |
Mus musculus |
Characteristics |
tissue: Brain cell type: Brain cells genotype: ApoE4 treatment: Old_aged
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
bulk_seq
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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
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Submission date |
Aug 30, 2022 |
Last update date |
Sep 15, 2022 |
Contact name |
Lance A Johnson |
E-mail(s) |
johnson.lancea@gmail.com
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Phone |
8593232746
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Organization name |
University of Kentucky
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Department |
Physiology/Sanders-Brown Center on Aging
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Street address |
760 Press Ave, HKRB 135
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City |
Lexington |
State/province |
KY |
ZIP/Postal code |
40536 |
Country |
USA |
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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 |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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