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Sample GSM7062064 Query DataSets for GSM7062064
Status Public on Oct 03, 2023
Title biol WT1
Sample type SRA
 
Source name Cortex
Organism Mus musculus
Characteristics tissue: Cortex
genotype: WT
Sex: male
Extracted molecule polyA RNA
Extraction protocol To isolate RNA, mouse cortex was homogenized in 1mL of TRIzol and RNA was purified using chloroform and Isopropyl alcohol
Poly(A)+ transcripts were isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module kit according to the manufacturer’s protocol (New England BioLabs Inc., Massachusetts, USA). RNA samples were randomly primed (5’ d(N6) 3’ [N=A,C,G,T]) and fragmented. The first strand was synthesized with Protoscript II Reverse Transcription with a modified extension period as to what is stated in the manufacturer’s protocol (30 minutes at 42⁰C). The remaining steps of library generation were carried out according to the manufacturer’s protocol NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description s182
Data processing RNA sequencing reads were trimmed using Trimmomatic/0.36. Illumina adapters were removed from the reads. The leading and trailing ends of reads were trimmed if the base quality dropped below a Phred score of 20, and a sliding window 4:15
Sequenced reads were aligned to the mouse genome mm10 using STAR/2.7.0f with the default parameters.
Genes with less than 20 reads were dropped and differential gene expression analysis was performed with DESeq2.
DESeq2 was also used to generate VST normalized read counts for each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
 
Submission date Feb 24, 2023
Last update date Oct 03, 2023
Contact name Matthew J Armstrong
E-mail(s) matthew.armstrong@emory.edu
Organization name Emory University
Street address 615 Michael St
City Atlanta
State/province Georgia
ZIP/Postal code 30322
Country USA
 
Platform ID GPL24247
Series (2)
GSE226053 Role of TET1-mediated epigenetic modulation in Alzheimer’s disease [RNA-Seq]
GSE226056 Role of TET1-mediated epigenetic modulation in Alzheimer's disease
Relations
BioSample SAMN33436011
SRA SRX19496131

Supplementary file Size Download File type/resource
GSM7062064_raw_counts_anno_s182_matrix.txt.gz 191.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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