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Status |
Public on Jan 20, 2023 |
Title |
hiPSC_dervied_ETV2positive_nonEC_day6 [D1_D6_SP] |
Sample type |
SRA |
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Source name |
hiPSC_dervied_ETV2positive_nonEC_day6
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Organism |
Homo sapiens |
Characteristics |
source cell line: ETV2 reporter hiPSC line cell type: hiPSC_dervied_ETV2positive_nonEC timepoint: day6
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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.
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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).
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Description |
FCHMV73BBXX_L1_WHHUMsdeEAAIRAAPEI-214
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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.
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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 |
|
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Platform ID |
GPL20301 |
Series (1) |
GSE157954 |
ETV2 Upregulation Marks the Specification of Early Cardiomyocytes and Endothelial Cells During Co-differentiation |
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Relations |
BioSample |
SAMN16133384 |
SRA |
SRX9124117 |