|
| Status |
Public on Jan 20, 2023 |
| Title |
hiPSC_dervied_ETV2positive_EC_day6 [D1_D6_DP] |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC_dervied_ETV2positive_EC_day6
|
| Organism |
Homo sapiens |
| Characteristics |
source cell line: ETV2 reporter hiPSC line
cell type: hiPSC_dervied_ETV2positive_EC
timepoint: day6
|
| Treatment protocol |
VEC+ cells with and withot ETV2+ expression were sorted on day 4, 5, 6, 8 of CMEC differentiation. Total RNA were extracted from all samples and sent for bulk RNAseq.
|
| Growth protocol |
CMEC differentiation was performed as follow: Briefly, 25 × 10^3 cells per cm2 were seeded on plates coated with 75 µg/ml matrigel growth factor reduced (Corning) the day before differentiation (day -1). At day 0, cardiac mesoderm was induced by changing E8 to BPEL medium (Bovine Serum Albumin [BSA] Polyvinyl alcohol Essential Lipids; 5, supplemented with a mixture of cytokines (20 ng/ml BMP4, R&D Systems; 20 ng/ml ACTIVIN A, Miltenyi Biotec; 1.5 μM GSK3 inhibitor CHIR99021, Axon Medchem). After 3 days, cytokines were removed and a Wnt inhibitor (5 μM XAV939, Tocris) and VEGF (50 ng/ml, R&D Systems) was added for 3 days. BPEL medium was refreshed every 3 days supplemented with VEGF (50 ng/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA for bulk samples was purified using the NucleoSpin RNA Kit (Bioke’) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
FCHMV73BBXX_L1_WHHUMsdeEAAJRAAPEI-216
|
| Data processing |
LUMC BIOPET Gentrap pipeline was used to process raw data (https://github.com/biopet/biopet). Trimming of low-quality read ends was done with Sickle (v1.2). Cutadapt (v1.1) was used for adapters clipping. Using GSNAP (gmap-2014-12-23) reads were aligned to the human reference genome GRCh38. Gene read quantification was done with with htseq-count (v0.6.1p1) against the Ensembl v87 annotation. The R package cqn (v1.24.0) was used to normalize gene length and GC content bias.
Genome_build: GRch38
Supplementary_files_format_and_content: RPKM_normalized_ETV2_bulk.csv: RPKM normalized based on gene length and GC content.
|
| |
|
| Submission date |
Sep 15, 2020 |
| Last update date |
Jan 20, 2023 |
| Contact name |
Valeria Orlova |
| E-mail(s) |
v.orlova@lumc.nl
|
| Organization name |
Leiden University Medical Center
|
| Street address |
Einthovenweg 20
|
| City |
Leiden |
| ZIP/Postal code |
2333ZC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE157954 |
ETV2 Upregulation Marks the Specification of Early Cardiomyocytes and Endothelial Cells During Co-differentiation |
|
| Relations |
| BioSample |
SAMN16133385 |
| SRA |
SRX9124116 |
