|
| Status |
Public on Jul 29, 2020 |
| Title |
CAFInhib1 |
| Sample type |
SRA |
| |
|
| Source name |
KPC cell line
|
| Organism |
Mus musculus |
| Characteristics |
treatment: miR-224 inhibitor
replicate: 1
cell type: CAF
|
| Treatment protocol |
miRNA lentiviral particles were purchased from GeneCopoeia with third generation technology for stable transduction
|
| Growth protocol |
Tumor cells, KPC CAFs, and PNAFs were maintained in RPMI 1640 with 10% FBS, 1 mM sodium pyruvate, 2 mM L-glutamine, 1% nonessential amino acids, penicillin (50 U/ml)/streptomycin (50 g/ml) (Life Technologies), and 0.2 U/ml human insulin (NovoLog) in a humidified incubator (37 degrees, 5% CO2)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction following stable transduction with RNAqueous micro kit
Illumina’s TruSeq Stranded Total RNA Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
CAFScr_vs_CAFInhib_all_isoforms_sorted.txt
|
| Data processing |
Illumina's CASAVA 1.8.4 was used to convert BCL files to FASTQ files
rsem-1.3.0 was used for running the alignments as well as generating gene and transcript expression levels.
rsem-1.3.0's EBSeq was used for Differential Expression analysis
Genome_build: RSEM version 1.3.0, aligned to reference genome mm10
|
| |
|
| Submission date |
Jan 08, 2020 |
| Last update date |
Jul 29, 2020 |
| Contact name |
Jacquelyn W Zimmerman |
| E-mail(s) |
[email protected], [email protected]
|
| Phone |
2566824782
|
| Organization name |
Johns Hopkins Sidney Kimmel Comp. Cancer Center
|
| Street address |
1650 Orleans St, Room 186
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21287 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE143326 |
Inhibition of miR-21 regulates mutant KRAS effector pathways and intercepts pancreatic ductal adenocarcinoma development |
|
| Relations |
| BioSample |
SAMN13795912 |
| SRA |
SRX7527433 |
