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| Status |
Public on Jul 09, 2023 |
| Title |
APP_B6_8M_C_rep2 |
| Sample type |
SRA |
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| Source name |
isolated microglia
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| Organism |
Mus musculus |
| Characteristics |
cell type: isolated microglia
genotype: App
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
DE_APP_B6_8M_C.WT_B6_8M_C.xlsx
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| 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
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| Submission date |
Jun 30, 2023 |
| Last update date |
Jul 09, 2023 |
| Contact name |
Akira Sobue |
| Organization name |
Nagoya university
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| Street address |
Furo-cho Chikusa-ku
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| City |
Nagoya |
| ZIP/Postal code |
464-8601 |
| Country |
Japan |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE236268 |
Microglial gene signature reveals loss of homeostatic microglia associated with neurodegeneration of Alzheimer's disease |
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| Relations |
| BioSample |
SAMN36176639 |
| SRA |
SRX20852411 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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