|
| Status |
Public on Jan 05, 2021 |
| Title |
BF2117: Acinar cell-derived tumor 2 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic tumor
|
| Organism |
Mus musculus |
| Characteristics |
genotype: KrasLSL-G12D/+;R26LSL-tdTom/LSL-tdTom;Ptf1aCreER; Trp53fl/fl
strain: mixed 129/Sv-C57BL/6
days after tamoxifen induction: 120
tissue: Pancreatic tumor
|
| Growth protocol |
Mouse models with the tamoxifen-inducible knock-in Ptf1aCreER allele or Sox9CreER transgene were used to express oncogenic KrasG12D and knockout Trp53 in mouse pancreatic acinar or ductal cells, respectively. At 8 – 10 weeks, mice were treated with tamoxifen and pancreatic tumors were isolated when mice reached morbidity.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
When mice reached morbidity, pancreatic tumors were micro-dissected and flash frozen in liquid nitrogen. RNA was extracted from bulk tumors using the RNeasy midi kit (Qiagen). RNA quality was assessed using a Bioanalyzer, and only samples with an RNA integrity number (RIN) greater than 8.0 were used for library preparation. RNA-seq libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina). The mRNA was enriched using oligo(dT) beads.
The mRNA is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were aligned to the GRCm38 mouse genome using HISAT2 Version 2.0.4
Sorted BAM files were generated using Samtools version 1.3.1.
The number of reads mapping to each gene in the mouse Ensembl database (version GRCm38.87) was counted using HTSeq-count version 0.6.1
Genes with less than 10 read counts in all samples were excluded from the analysis.
Differential gene expression analysis was performed using DESeq2 version 1.24.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw gene counts for each gene in every sample
Supplementary_files_format_and_content: DESeq2 Output
|
| |
|
| Submission date |
Jan 04, 2021 |
| Last update date |
Jan 06, 2021 |
| Contact name |
Brittany Maria Flowers |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Department of Radiation Oncology
|
| Lab |
Laura Attardi
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE164180 |
Gene expression profiling of mouse pancreatic tumors derived from acinar or ductal cells |
|
| Relations |
| BioSample |
SAMN17208663 |
| SRA |
SRX9773844 |
