|
| Status |
Public on Apr 19, 2024 |
| Title |
biol rep 1- pancreatic control wt acinar cells (WT_24) |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic acinar cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: pancreatic acinar cells
developmental stage: adult
genotype: Pdx1Cre;Trip12+/+
treatment: none
|
| Treatment protocol |
no treatment
|
| Growth protocol |
the tumor murine cell lines were grown in DMEM/F12 medium (Gibco-BRL) supplemented with 10% fetal calf serum, antifungics and antibiotics in humidified atmosphere with 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were isolated using Trizol reagent (Life Technologies) following manufacturer's recommendations. Preliminary quality control of total mRNA was ensured by agarose gel electrophoresis and NanoDrop measurement. Sample quantitation and integrity were performed by Nanodrop and Agilent 2100, respectively.
mRNA libraries were constructed using poly A enrichment preparation. 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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
read alignment on Mouse_GRCm39 version 2.7.4a indexed genome with STAR version 2.7.10a
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GrCM39/mm39 using STAR version 2.7.10a
Read count extraction and normalization were performed using STAR version 2.7.10a
Assembly: mm39
Supplementary files format and content: tab-delimited text files include count values for each Sample
|
| |
|
| Submission date |
Dec 22, 2022 |
| Last update date |
Apr 19, 2024 |
| Contact name |
Marlène DUfresne |
| E-mail(s) |
marlene.dufresne@inserm.fr
|
| Organization name |
Inserm
|
| Lab |
CRCT
|
| Street address |
2 Avenue Hubert Curien
|
| City |
Toulouse |
| ZIP/Postal code |
31037 |
| Country |
France |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE221587 |
Effect of depletion of TRIP12 on gene expression in adult murine pancreatic acinar cells and murine pancreatic cancer cell lines |
|
| Relations |
| BioSample |
SAMN32368579 |
| SRA |
SRX18824176 |
