|
| Status |
Public on Apr 20, 2024 |
| Title |
PANC1 LM3 cells shNPTX1_3 biological replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
liver metastasizing pancreatic ductal carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: liver metastasizing pancreatic ductal carcinoma
cell line: PANC1 LM3
cell type: pancreatic cancer
genotype: NPTX1 knock down
|
| Growth protocol |
500,000 cells of each cells (shCTRL, shNPTX1_3, and shNPTX1_4 expressing PANC1 LM3 cells) were injected into the spleen on day 1 and liver metastazing tumors were harvested on day 21
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from ex vivo liver metastasizing tumors using Norgen's total RNA purification kit
Using Truseq RNA library prep kit Ver2, the manufacture's protocol has been followed
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
PANC1 liver metastatic 3rd generation (PANC1 LM3) shNPTX1_3 3
|
| Data processing |
mRNA reads were aligned to human or mouse reference genome (hg19 or mm39) with STAR 2.7.6a using the default setting (Dobin et al., 2013). To quantify gene expression, we counted sequenced reads mapping to exon regions using featureCounts v2.0.0 (Liao et al., 2014). The sequencing and mapping quality were examined with MultiQC v1.9 (Ewels et al., 2016). Differential expression analysis was performed using DESeq2 v1.24 (Love et al., 2014).
Assembly: hg19
Supplementary files format and content: excel spread sheet with the differential gene expression analysis results
|
| |
|
| Submission date |
Apr 20, 2022 |
| Last update date |
Apr 20, 2024 |
| Contact name |
Norihiro Yamaguchi |
| E-mail(s) |
norihiro.yamaguchi@mac.com, nyamaguchi@rockefeller.edu
|
| Phone |
1-212-327-7210
|
| Organization name |
The Rockefeller University
|
| Department |
Systems Cancer Biology
|
| Lab |
Tavazoie
|
| Street address |
1230 York Avenue, Box 16
|
| City |
New York |
| State/province |
Ny |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE201176 |
Transcriptomic profiling of highly- and lowly- metastasizing pancreatic ductal carcinoma cells [mRNAseq shNPTX1] |
| GSE201177 |
Transcriptomic profiling of highly- and lowly- metastasizing pancreatic ductal carcinoma cells |
|
| Relations |
| BioSample |
SAMN27676936 |
| SRA |
SRX14938547 |
