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| Status |
Public on Feb 04, 2024 |
| Title |
WT_317245 |
| Sample type |
SRA |
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| Source name |
Hippocampus
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| Organism |
Sus scrofa |
| Characteristics |
tissue: Hippocampus
genotype: WT
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hippocampal tissue from four WT pigs, four PS1 pigs and four APP/PS1 pigs were quickly removed after sacrificing the animals, dissected on ice and immediately submerged into liquid nitrogen and stored at -135oC. Tissues were homogenized in 1mL cold homogenization buffer (20mL Thioglycerol per millilitre of Homogenization solution) using a blender. Homogenates were left to settle on ice. Homogenates (200mL) were mixed with equal volume Lysis buffer and added to cartridges (Maxwell® 16 LEV simplyRNA Tissue Kit; Promega). DNAse I solution was added before samples were processed on Maxwell ® 16 Instrument. Eluted RNA was stored in -70oC.
Library construction, sequencing and initial data filtering including adaptor removal were performed by BGI Europe Genome Center. Total RNA was subjected to oligo dT based mRNA enrichment. 100 bp paired-end read sequencing was performed on BGIseq-500 with DNBseq technology. More than 20 million clean reads were obtained per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Reads were aligned to the porcine genome build Sscrofa11.1 (Ensemble release 92) using HISAT2 aligner (v2.1.0)
Transcript quantification was performed using htseq-count (v0.9.1)
Read counts were normalized for effective gene length, and sequencing depth to yield Transcripts Per Kilobase Million (TPM)
Differentially expressed genes were determined from count tables using DEseq2 (v2.11.40.6)
Assembly: Sscrofa11.1 (Ensemble release 92)
Supplementary files format and content: tab-delimited file containing TPM values for each sample
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| Submission date |
Jan 30, 2024 |
| Last update date |
Feb 04, 2024 |
| Contact name |
Per Qvist |
| E-mail(s) |
per.q@biomed.au.dk
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| Phone |
50192006
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| Organization name |
Aarhus University
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| Department |
Biomedicine
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| Street address |
Høegh-Guldbergs Gade 10
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| City |
Aarhus c |
| State/province |
Danmark |
| ZIP/Postal code |
8000 |
| Country |
Denmark |
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| Platform ID |
GPL26285 |
| Series (2) |
| GSE254548 |
APP and its intracellular domain modulate Alzheimer’s disease risk gene networks in transgenic APPsw and PSEN1M146I porcine models [hippocampus] |
| GSE254571 |
APP and its intracellular domain modulate Alzheimer’s disease risk gene networks in transgenic APPsw and PSEN1M146I porcine models |
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| Relations |
| BioSample |
SAMN39671299 |
| SRA |
SRX23448274 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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