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Sample GSM5660526 Query DataSets for GSM5660526
Status Public on Oct 02, 2023
Title 5AD_ApoEsiRNA_2Week_F_A5
Sample type SRA
 
Source name Brain (Cortex)
Organism Mus musculus
Characteristics tissue: Brain (Cortex)
treatment: Apoe siRNA
collection time post-treatment: 2 Weeks
injection: Bilateral Intracerebroventricular
scaffold/conjugate: Divalent siRNA
strain: 5XFAD
Treatment protocol Mice were injected with either a non-targeting control siRNA or a mouse Apoe targeting siRNA
Growth protocol Mice were fed on a normal chow diet
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using the NEB Monarch Total RNA Miniprep Kit (T2010S) with the protocol to purify long as well as short RNAs
Sequencing libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep kit (Illumina cat# 20020595) according to the manufacterers protocol. Briefly, PolyA RNA was purified with oligo-dT beads. This RNA was fragmented and first and second strand cDNA was synthesized. 3' cDNA ends were adenylated, adapters were ligated, and the library PCR was performed. library quality was checked using a Bioanalyzer High Sensitivity DNA kit (Agilent cat# 5067-4626). Libraries were purified from adapter dimers by gel extraction. Final libraries were quantified using the KAPA Library Quantification kit (Roche cat# 07960140001) according to the manufacterer's protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model NextSeq 550
 
Description Brain_5AD_norm_counts.csv
Data processing FASTQ files were mapped to the mouse genome using STAR v2.7.6e with default settings. Custom .gtf files were used for each Alzheimer's mouse model.
Transcripts were quantified using RSEM v1.3.3 using default settings.
Libraries were normalized and differential expression analysis was performed using DESeq2 v1.22.2 with apeglm shrinkage and alpha=0.05
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts data from DESeq2 are provided as .csv files. Metadata files for DESeq2 analysis are provided as .csv files.
 
Submission date Oct 28, 2021
Last update date Oct 02, 2023
Contact name Samuel Hildebrand
E-mail(s) samuel.hildebrand@umassmed.edu
Organization name University of Massachusetts Medical School
Department RNA Therapeutics Institute
Lab Khvorova
Street address 368 Plantation Street
City Worcester
State/province MA
ZIP/Postal code 01605
Country USA
 
Platform ID GPL21626
Series (1)
GSE186756 mRNA sequencing of brain and liver in multiple Alzheimer's Disease mouse models after treatment with either a Non-Targeting Control siRNA or an siRNA targeting mouse Apoe mRNA
Relations
BioSample SAMN22645374
SRA SRX12812695

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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