|
| Status |
Public on Apr 19, 2023 |
| Title |
PDO#1_xenograft_ROR1high-2 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PDO#1 (human pancreatic adenocarcinoma)
model: xenograft
sorted cell: ROR1high
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from sorted ROR1high and ROR1low cells using MagMAX-96 Total RNA Isolation Kit (Thermo Fisher Scientific), and 1 ng of RNA was used for the reverse transcription reaction using SMART-seq HT (Takara).
RNA-seq library was prepared using Nextera XT Library Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls and conversion to FASTQ files were performed using Basesapce online (Illumina).
Sequencing reads were trimmed for adaptor sequence, and aligned to human transcriptome (GRCh37) and quantified with Salmon (version 1.3.0) with default settings.
Differential expression testing was performed with DESeq2 (version 1.28.1).
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for every gene and every sample.
Supplementary_files_format_and_content: Tab-delimited text files include p-value and q-value for every genes.
|
| |
|
| Submission date |
Jan 10, 2022 |
| Last update date |
Apr 19, 2023 |
| Contact name |
Masaya Yamazaki |
| E-mail(s) |
myamazaki@kumamoto-u.ac.jp
|
| Organization name |
Kumamoto university
|
| Lab |
Medical Biochemistry
|
| Street address |
1-1-1, Honjyo, Chuo-ku
|
| City |
Kumamoto city |
| ZIP/Postal code |
860-8556 |
| Country |
Japan |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE191198 |
Single-cell RNA-sequencing reveals an intratumor heterogeneity in pancreatic adenocarcinoma [RNA-seq] |
| GSE191204 |
Single-cell RNA-sequencing reveals an intratumor heterogeneity in pancreatic adenocarcinoma |
|
| Relations |
| BioSample |
SAMN24804930 |
| SRA |
SRX13698742 |
