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Status |
Public on Oct 02, 2023 |
Title |
5AD_ApoEsiRNA_2Week_F_A5 |
Sample type |
SRA |
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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.
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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.
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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 |