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| Status |
Public on Feb 04, 2024 |
| Title |
Minipigno.558APP/PS1 so2709P5-γinhibition (2uM) |
| Sample type |
SRA |
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| Source name |
Ear biopsy
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| Organism |
Sus scrofa |
| Characteristics |
tissue: Ear biopsy
cell type: Fibroblasts
genotype: APP/PS1
treatment: 2uML-685-458 (g-secretase inhibitor)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Porcine fibroblasts were obtained from ear biopsies from WT, PS1 and APP/PS1 Göttingen minipigs and cultured in porcine fibroblast medium (Dulbecco’s Modified Eagle’s Medium (DMEM; Sigma Aldrich), 10% FBS (Life Technologies), 1% P/S (P/S, 10,000 units/mL and 10,000μg/mL; Life Technologies), 1% Gln (2.92g/100mL) and 6.667ng/mL Fibroblast Growth Factor-basic (bFGF; Life Technologies)) in 5% CO2 in a humidified chamber at 37oC. Established fibroblasts were split in a 1:3 ratio every 3 days using 0.05% trypsin EDTA (Life Technologies). All fibroblasts used in this study were tested negative for mycoplasma (MYCOPLASMACHECK, Eurofins Genomics).
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. 50 bp single-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) |
| GSE254570 |
APP and its intracellular domain modulate Alzheimer’s disease risk gene networks in transgenic APPsw and PSEN1M146I porcine models [fibroblasts] |
| 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 |
SAMN39672206 |
| SRA |
SRX23449877 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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