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| Status |
Public on Jun 17, 2024 |
| Title |
Ptf1aERT;Pdx1f/f, replicate 1 |
| Sample type |
SRA |
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| Source name |
Pancreatic acinar cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Pancreatic acinar cells
time: 2 weeks after Tamoxifen
gender: Female
genotype: Ptf1aERT;Pdx1f/f
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| Treatment protocol |
To induce Ptf1aCreERT-dependent recombination, animals were treated with Tamoxifen (T5648, Sigma). Tamoxifen was dissolved in corn oil and administered by oral gavage, 5mg daily for a total of five days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For acinar cell isolation, pancreas tissue was washed three times in Hank’s Balanced Salt Solution (HBSS) (SH3026801, Thermo Fisher Scientific), minced and digested in HBSS containing 0.5mg/ml Collagenase P (Roche, 11249002001) for 15 minutes at 37°C. Digestion reaction was stopped by washing the tissue three times in HBSS with 5% FBS. Acinar cells were isolated by straining the tissue through 500µm and 100µm filter meshes and centrifugating the cells through a gradient of 30% FBS in HBSS. For total RNA extraction, the RNeasy® Plus Mini Kit (74134, Qiagen) was used following manufacturer’s instructions.
Library preparation and sequencing was performed at the Advanced Genomics Core of the University of Michigan. Library was constructed using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequencing reads were assessed for quality metrics using FastQC and multiQC. Reads were aligned to the mouse reference genome (GRCm38/mm10 Ensembl release 98) using Salmon.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
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| Submission date |
Jan 22, 2024 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Simone Benitz |
| Organization name |
Henry Ford Health System
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| Street address |
2799 W Grand Blvd
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| City |
Detroit |
| ZIP/Postal code |
48202 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE253600 |
ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma |
| GSE253927 |
ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma [RNA-seq isoAC] |
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| Relations |
| BioSample |
SAMN39551792 |
| SRA |
SRX23354775 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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