|
| Status |
Public on Feb 22, 2020 |
| Title |
NR5A1-DOX (+)_CHIR_RNA-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
CHIR-treated NR5A1-DOX (+) cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human embryonic stem cells (H9)
culture condition: CHIR condition
genotype: NR5A1 overexpression
|
| Growth protocol |
Parental-DOX (+) cells were cultured in mTeSR1 with doxycycline (DOX) on Matrigel-coated dishes. CHIR-treated NR5A1-DOX (+) cells were cultured in custom mTeSR1 lacking FGF2 and TGF-β with DOX and 3 µM CHIR99021 on Matrigel-coated dishes.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol-LS Reagent. RNA integrity was evaluated using an Agilent 2100 Bioanalyzer with an Agilent 6000 RNA Pico Kit.
Libraries for Miseq sequencing were prepared using a TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to the manufacturer’s instructions. After adapter ligation, purified cDNA was amplified by 15 cycles of PCR. The libraries were evaluated using the Agilent 2100 Bioanalyzer with an Agilent High-Sensitivity DNA Kit. The validated libraries were loaded into Miseq Reagent Kit v3 (150 cycles) at a final concentration of 10 pM, and sequencing was performed in a Miseq sequencer (Illumina) using the paired end mode.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
All RNA-seq datasets including in this study were aligned using STAR (version 2.5.3) to the human genome (UCSC hg19) with 50 bp single-end mode and command options for 2-pass and unique mapping. The count data were obtained using htseq-count in HTSeq (version 0.9.1) with annotation from UCSC hg19. Reads per kilobase of exon per million mapped fragments (RPKM) were calculated by the R project (version 3.3.1). Genome build: hg19. A text file including RPKM values for each sample is provided.
|
| |
|
| Submission date |
Jul 10, 2017 |
| Last update date |
Feb 22, 2020 |
| Contact name |
Hirofumi Suemori |
| E-mail(s) |
hsuemori@infront.kyoto-u.ac.jp
|
| Phone |
81-75-751-3821
|
| Organization name |
Kyoto University
|
| Department |
Institute for Frontier Life and Medical Sciences
|
| Lab |
Embryonic Stem Cell Research
|
| Street address |
53 Kawaharacho, Shogoin, Sakyo-ku
|
| City |
Kyoto |
| ZIP/Postal code |
606-8505 |
| Country |
Japan |
| |
|
| Platform ID |
GPL15520 |
| Series (2) |
| GSE101088 |
Overexpression of nuclear receptor 5A1 induces and maintains an intermediate state of conversion between primed and naive pluripotency |
| GSE101089 |
Overexpression of nuclear receptor 5A1 induces and maintains an intermediate state of conversion between primed and naive pluripotency |
|
| Relations |
| BioSample |
SAMN07339373 |
| SRA |
SRX2993679 |
