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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 17, 2021 |
| Title |
CTRL #01 |
| Sample type |
SRA |
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| Source name |
Pancreatic spheroids
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| Organism |
Mus musculus |
| Characteristics |
cell type: Pancreatic epithelial cells
treatment: Untreated
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| Treatment protocol |
See additional columns of the SAMPLES section
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| Growth protocol |
DMEM/F12 1:1 supplemented with 2.5 mM L-Glutamine, 15 mM HEPES Buffer (HyClone), 5 mg/ml D-glucose (Sigma Aldrich), 1.22 mg/ml nicotinamide (Sigma Aldrich), 5 nM 3,3,5-Tri-iodo-L-thyronine (Sigma Aldrich), 0.5 μM hydrocortisone Solution (Sigma Aldrich), 100 ng/ml cholera toxin (Sigma Aldrich), 0.5 % insulin-transferrin-selenium (Corning), 100 μg/ml penicillin/streptomycin (Gibco), 0.1 mg/ml soybean trypsin inhibitor (Sigma Aldrich), 20 ng/ml EGF (Peprotech), 25 μg/ml bovine pituitary extract (Invitrogen), and 5% Nu Serum IV Culture Supplement (BD)
See additional columns of the SAMPLES section
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| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina Truseq. The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
genes.counts.txt
genes.edgeR_results.txt
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| Data processing |
Reads were quality filtered according to the Illumina pipeline, then were aligned to mouse genome build GRCm38/mm10 using using START version 2.6.0c. Only uniquely mapped reads were retained.
Gene expression counts were estimated using featureCounts v0.6.1 (Rsubread version 1.6.1) , summarized across all exons , with option “largestOverlap”.
Differentially expressed genes were identified using EdgeR R-package v3.2.2.
Genome_build: GRCm38/mm10
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| Submission date |
Jul 15, 2021 |
| Last update date |
Sep 17, 2021 |
| Contact name |
Chiara Balestrieri |
| E-mail(s) |
balestrieri.c@gmail.com
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| Organization name |
IRCCS San Raffaele Scientific Institute
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| Department |
Center for Omics Sciences
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| Street address |
Via Olgettina 58
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| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE180211 |
Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis [RNA-seq] |
| GSE180212 |
Epithelial memory of resolved inflammation limits tissue damage while promoting pancreatic tumorigenesis |
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| Relations |
| BioSample |
SAMN20251862 |
| SRA |
SRX11473377 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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