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Sample GSM7865810 Query DataSets for GSM7865810
Status Public on Nov 15, 2023
Title P301L_2
Sample type SRA
 
Source name Primary cultured neurons
Organism Mus musculus
Characteristics cell type: Primary cultured neurons
genotype: WT
treatment: AAV-P301L
Extracted molecule total RNA
Extraction protocol RNA was harvested using Direct-zol RNA Microprep Kits
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Quality control: Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: Text files include average count number for each group
 
Submission date Oct 25, 2023
Last update date Nov 15, 2023
Contact name Wei Cao
E-mail(s) [email protected]
Organization name The University of Texas Health Science Center at Houston
Street address 6431 Fannin Street
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL17021
Series (1)
GSE246259 MAPK-DLK signaling coupled with DNA damage promotes intrinsic neurotoxicity associated with non-mutated tau
Relations
BioSample SAMN37985997
SRA SRX22229260

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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