|
| Status |
Public on Jun 06, 2021 |
| Title |
RNA-seq_D0_CTCF_p42_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Human induced pluripotent stem cell (hiPSC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: ZIP13K2
differentiation days: Day 0
genotype: SOX17(delta5'CTCF)
cxcr4 status: n/a
|
| Growth protocol |
ZIP13K2 cultures were treated with Accutase (Sigma-Aldrich, A6964) supplemented by 10 µM Y-27632 (Tocris, 1254) to obtain single cells. To quench and wash the cells, equal volumes of mTeSR1 (Stemcell Technologies) were added and cells spun down for 5 min. at 300 x g, 21°C. After resuspension in mTeSR1 supplemented by 10 µM Y-27632, cells were counted and seeded according to the manufacturer’s instructions on Matrigel (Corning) pre-coated culture plates / dishes. Media change using the STEMdiff Trilineage Endoderm Differentiation media (Stemcell Technologies) was performed on a daily base after washing the cultures with equal volumes of DPBS (Thermo Fischer Scientific, 14190250) according to the manufacturer’s instructions. Triplicates of either undifferentiated or differentiated ZIP13K226 cultures were treated with Accutase® (Sigma-Aldrich, A6964) and differentiated cultures were further quenched with FACS-buffer containing 5 mM EDTA (ThermoFischer Scientific, 15575020) 10% Fetal bovine serum (FBS) (ThermoFischer Scientific, 26140079) in DPBS (Thermo Fischer Scientific, 14190250). In order to enrich for CXCR4- or CXCR4+ cell fractions of differentiated cultures, cells were stained for anti-Human CRCX4 (CD184) PE (as described under 21. FACS) and compared to Isotype and unstained control sorted for either CXCR4- or CXCR4+ on the Aria II (Beckton Dickinson).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA isolation including on-column DNase digest of enriched cell populations was performed using the RNeasy Mini Kit (Qiagen, 74104) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
SOX17 upstream TIR boundary CTCF knockout
|
| Data processing |
Gene counts are quantified by using RSEM default parameters with REFSEQ annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Gene quantification files (*.genes.results.txt) are generated using RSEM
|
| |
|
| Submission date |
Feb 26, 2019 |
| Last update date |
Jun 06, 2021 |
| Contact name |
Hua-Jun Wu |
| E-mail(s) |
hjwu@pku.edu.cn
|
| Organization name |
Peking University Health Science Center
|
| Department |
School of Basic Medical Sciences
|
| Lab |
Center for Precision Medicine Multi-Omics Research
|
| Street address |
8 science park road, zhongguancun life science park
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE127194 |
Topological isolation as a mechanism for precise control of developmental regulators in mammalian genomes [RNA-seq] |
| GSE127196 |
Topological isolation as a mechanism for precise control of developmental regulators in mammalian genomes |
|
| Relations |
| BioSample |
SAMN11022372 |
| SRA |
SRX5431625 |
