|
| Status |
Public on Jun 17, 2024 |
| Title |
HPAF-II, ROR2, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
HPAF-II
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HPAF-II
cell type: Pancreatic cancer cell line
|
| Growth protocol |
HPAF-II cells were cultured in Minimum Essential Medium containing 1% sodium pyruvate , 1% non-essential amino acids, 10% FBS and 0.5% Gentamicin. UM32 were cultivated in RPMI 1640 supplemented with 10% FBS and 0.5% Gentamicin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA extraction, the RNeasy® Plus Mini Kit (74134, Qiagen) was used following manufacturer’s instructions. Genomic DNA was digested on column by using the RNase-Free DNase Set (79254, Qiagen).
Library preparation and sequencing was performed at MedGenome Inc.. RNA-seq library preparation was performed by using the Illumina TruSeq stranded mRNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapter trimming and removal of ribosomal and mitochondrial genome was carried out with fastq-mcf, cutadapt and Bowtie2, respectively. Reads were mapped to the hg19 genome using STAR and raw read counts were estimated with HTSeq (v0.11.2) and normalized with DESeq2.
Assembly: hg19
Supplementary files format and content: RawNormCounts_ROR2.txt
|
| |
|
| Submission date |
Jan 18, 2024 |
| Last update date |
Jun 17, 2024 |
| Contact name |
Simone Benitz |
| Organization name |
Henry Ford Health System
|
| Street address |
2799 W Grand Blvd
|
| City |
Detroit |
| ZIP/Postal code |
48202 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE253599 |
ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma (RNA-Seq) |
| GSE253600 |
ROR2 regulates cellular plasticity in pancreatic neoplasia and adenocarcinoma |
|
| Relations |
| BioSample |
SAMN39486488 |
| SRA |
SRX23277812 |
