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Status |
Public on Nov 15, 2023 |
Title |
P301L_2 |
Sample type |
SRA |
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Source name |
Primary cultured neurons
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Organism |
Mus musculus |
Characteristics |
cell type: Primary cultured neurons genotype: WT treatment: AAV-P301L
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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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
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Submission date |
Oct 25, 2023 |
Last update date |
Nov 15, 2023 |
Contact name |
Wei Cao |
E-mail(s) |
[email protected]
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Organization name |
The University of Texas Health Science Center at Houston
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Street address |
6431 Fannin Street
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City |
Houston |
State/province |
Texas |
ZIP/Postal code |
77030 |
Country |
USA |
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Platform ID |
GPL17021 |
Series (1) |
GSE246259 |
MAPK-DLK signaling coupled with DNA damage promotes intrinsic neurotoxicity associated with non-mutated tau |
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Relations |
BioSample |
SAMN37985997 |
SRA |
SRX22229260 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
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