{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Yukiyasu Komaki"],"organism":["Mus musculus"],"software":["R v4.5.1; DESeq2 v1.48.2","Trimmomatic v0.39; FastQC v0.11.9; HISAT2 v2.2.1; featureCounts v2.0.8"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16606"],"description":["Bulk RNA sequencing of hippocampal tissue was conducted to investigate transcriptomic alterations associated with amyloid-β (Aβ) seeding in vivo. Hippocampi were obtained from 17-month-old hAβ-KI mice that had undergone unilateral intrahippocampal injection of Aβ seeds into the left hippocampus 12 months prior, while the contralateral right hemisphere received PBS as a control (n = 3). Hippocampal samples from both the left (Aβ seed-injected) and right (PBS-injected) hemispheres were collected simultaneously and subjected to bulk RNA-seq analysis. Total RNA was purified using RNeasy Plus Mini Kit (QIAGEN), followed by preparation of poly(A)-enriched, strand-specific RNA-seq libraries. Sequencing was performed in a paired-end manner on a next-generation sequencing platform, yielding approxi"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Hippocampal tissues were collected from 17-month-old hAβ-KI mice that had received unilateral intrahippocampal injection of Aβ seed (left) and PBS (right) 12 months earlier. Hippocampi were excised, snap-frozen in liquid nitrogen, and stored at −80 °C.","Library Construction - Poly(A)-selected, strand-specific RNA-seq libraries were prepared with the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).","Sequencing - Sequencing was performed on an Illumina NovaSeq X Plus to obtain approximately 40 million 150 bp paired-end reads per sample by Rhelixa, Inc. (Tokyo, Japan).","Nucleic Acid Extraction - Total RNA was isolated from hemihippocampal tissue using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s instructions."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw read counts were normalized using the DESeq2 package (v1.48.2) in R (v4.5.1). Differential expression analysis was performed using a paired design, and p-values were adjusted using the Benjamini–Hochberg method.","Sequence Alignment - Adapter trimming was conducted with Trimmomatic v0.39, and read quality was assessed using FastQC v0.11.9. Clean reads were aligned to the mouse reference genome (UCSC mm10, GRCm38) using HISAT2 v2.2.1. Gene-level read counts were generated using featureCounts v2.0.8."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["PC","Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Yukiyasu Komaki"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq analysis of hippocampal tissue from hAβ-KI mice injected with Amyloid β seed or PBS","description":"Bulk RNA sequencing of hippocampal tissue was conducted to investigate transcriptomic alterations associated with amyloid-β (Aβ) seeding in vivo. Hippocampi were obtained from 17-month-old hAβ-KI mice that had undergone unilateral intrahippocampal injection of Aβ seeds into the left hippocampus 12 months prior, while the contralateral right hemisphere received PBS as a control (n = 3). Hippocampal samples from both the left (Aβ seed-injected) and right (PBS-injected) hemispheres were collected simultaneously and subjected to bulk RNA-seq analysis. Total RNA was purified using RNeasy Plus Mini Kit (QIAGEN), followed by preparation of poly(A)-enriched, strand-specific RNA-seq libraries. Sequencing was performed in a paired-end manner on a next-generation sequencing platform, yielding approxi","dates":{"release":"2026-09-30T00:00:00Z","modification":"2026-09-30T01:00:37.459Z","creation":"2026-02-09T11:12:57.458Z"},"accession":"E-MTAB-16606","cross_references":{"ENA":["ERP188870"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}