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Sample GSM7525873 Query DataSets for GSM7525873
Status Public on Jul 09, 2023
Title WT_B6_8M_C_rep3
Sample type SRA
 
Source name isolated microglia
Organism Mus musculus
Characteristics cell type: isolated microglia
genotype: WT
Extracted molecule total RNA
Extraction protocol For the RNA-seq of the mouse samples, total RNA was extracted from MACS-isolated microglia of each models using an RNeasy Micro Kit (Qiagen, Hilden, Germany). The RNAs were sampled from cerebral cortices of 8-month-old AppNL-G-F/NL-G-F and 7-month-old rTg4510 mice and lumbar spinal cords of 5-month-old SODG93A mice together with the corresponding wild-type or non-Tg control mice, respectively.
Libraries were prepared by using TruSeq mRNA or TruSeq Stranded mRNA (Illumina, San Diego, CA, USA), and, from these libraries, 151-nt paired-end reads were sequenced on the HiSeq X Ten with the HiSeq X Reagent Kits (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description DE_APP_B6_8M_C.WT_B6_8M_C.xlsx
Data processing The reference genome assemblies and gene annotations, the mouse genome version UCSC mm10 were retrieved from iGenomes
The Illumina adapter sequences, as well as low quality bases (quality score < 20), were trimmed from 3’-ends of the sequencing reads with the Trim Galore v0.5.0
The reads were qualified with FastQC v0.11.8 before and after trimming.
The processed reads were mapped on the reference genome assembly with HISAT2 v2.1.0
Mapping reads prepared with the stranded kit was processed by employing strand specificity information. The alignments on rDNA regions were removed with BEDTools v2.25.0. From mapping data, expressions of the individual annotated genes were quantified with StringTie v1.3.5
Assembly: mm10
Supplementary files format and content: MS Excel file including CPM values of the individual genes for each sample and the results of the differential expression analysis
 
Submission date Jun 30, 2023
Last update date Jul 09, 2023
Contact name Akira Sobue
Organization name Nagoya university
Street address Furo-cho Chikusa-ku
City Nagoya
ZIP/Postal code 464-8601
Country Japan
 
Platform ID GPL21273
Series (1)
GSE236268 Microglial gene signature reveals loss of homeostatic microglia associated with neurodegeneration of Alzheimer's disease
Relations
BioSample SAMN36176642
SRA SRX20852408

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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