|
| Status |
Public on Apr 01, 2024 |
| Title |
Pt1 iPSC-HPCs, KRASG13C, stimulated_SF |
| Sample type |
SRA |
| |
|
| Source name |
induced pluripotent stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: hematopoietic progenitor cells
patient: patient_1
genotype: WT/K13C
treatment: cultured_with_cytokines_SF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using NucleoSpinRNA XS kit (MACHEREY-NAGEL). 1-10 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Genedata Profiler Genome (GPG) v 11.0.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using GPG workflow.
Trimmed sequence reads (100bp) were mapped to GRCh37/hg19 using GPG and STAR sotwares.
Read count extraction and normalization were performed using GPG and STAR workflow.
All the above procedures were performed by TAKARA Bio.
Assembly: hg19
Supplementary files format and content: Excel spreadsheet files include FPKM values and read counts for each sample
|
| |
|
| Submission date |
Apr 11, 2022 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Makoto Otsu |
| E-mail(s) |
motsu@med.kitasato-u.ac.jp
|
| Organization name |
Kitasato University School of Medicine
|
| Street address |
1-15-1 Kitasato, Minami-ku
|
| City |
Sagamihara |
| State/province |
Kanagawa |
| ZIP/Postal code |
252-0374 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE200600 |
Effects of KRAS (G13C) expression on transcriptome profiles assessed in HPCs differentiated from patient-derived iPS cells |
|
| Relations |
| BioSample |
SAMN27518365 |
| SRA |
SRX14814352 |
