|
| Status |
Public on Oct 17, 2023 |
| Title |
N_D3_2F_H9_2 |
| Sample type |
SRA |
| |
|
| Source name |
2F D3 naïve H9(PDGFRA positive)_2
|
| Organism |
Homo sapiens |
| Characteristics |
analysis method: RNA-seq
cell line: H9
cell type: 2F naive PSC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using miRNeasy Mini Kit (QIAGEN)
To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls were performed using bcl2fastq v2.17.1.14.
Low quality bases and adapters in sequenced reads were trimmed with cutadapt-1.15
The sequenced reads were mapped to the hg38 human reference genome and the EGFP sequence using Tophat2 (version 2.1.1) with the human GENCODE (version 27) annotation gtf file.
The mapped reads with high mapping quality (MAPQ >= 20) were used for further analyses.
FPKM values were determined by Cufflinks version 2.2.1 package with the human GENCODE (version v27) annotation gtf file.
Genome_build: hg38
Supplementary_files_format_and_content: The tab-delimited text file include FPKM values for each sample.
|
| |
|
| Submission date |
Dec 07, 2020 |
| Last update date |
Feb 28, 2024 |
| Contact name |
Yasuhiro Takashima |
| E-mail(s) |
y.takashima@cira.kyoto-u.ac.jp
|
| Phone |
0081-75-366-7193
|
| Organization name |
Kyoto University
|
| Street address |
53 Kawahara-cho, Shogoin, Sakyo-ku
|
| City |
Kyoto |
| ZIP/Postal code |
606-8507 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE131747 |
Hypoblast from human pluripotent stem cells regulates epiblast development |
| GSE233959 |
Hypoblast from human pluripotent stem cells regulates epiblast development [RNA-seq] |
|
| Relations |
| BioSample |
SAMN17016091 |
| SRA |
SRX20852024 |
