|
| Status |
Public on Oct 17, 2023 |
| Title |
GATA6 o/e D1 naïve H9(PDGFRA positive)_2 |
| Sample type |
SRA |
| |
|
| Source name |
H9 ESCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9 ESCs
treatment: PDGFRA+ cells at day 1 after GATA6 overexpression in naive PSCs
|
| Growth protocol |
Primed human PSCs were maintained on MEF under DMEM/F12 with 20% KSR, 1% NEAA, 4 ng/ml bFGF and 0.1 mM 2-ME. Naïve human PSCs were maintained on MEF with t2iLGo medium, which consists of N2B27 (Ndiff227) with 1 uM PD0325901, 1 uM CHIR99021, 10 ng/ml hLIF and 3 uM Go6983. GATA6 was overexpressed in naïve and primed PSCs. PDGFRA+ cells were sorted at day 1 and 3. As another samples, 7 factors were added in naïve PSCs. PDGFRA positive cells were collected at day 3. 7 factors: 25 ng/ml FGF4, 1 ug/ml heparin sodium, 10 ug/ml recombinant human BMP4, 10 ng/ml recombinant human PDGF-AA, 1 uM XAV939, 3 uM A83-01, 0.1 uM retinoic acid, and 10 ng/ml recombinant human IL-6
|
| 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 |
| |
|
| Description |
N_D1_G6_H9_2
N_G6_D1_PRA_ex2
|
| 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 |
May 24, 2019 |
| 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 |
SAMN11845787 |
| SRA |
SRX20851996 |
