|
| Status |
Public on Jan 01, 2020 |
| Title |
H9_ESC |
| Sample type |
SRA |
| |
|
| Source name |
ESC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
cell type: ESC
gender: female
day: n/a
|
| Treatment protocol |
For RNA purification, vascular organoids were treated for 1h with 3U/mL Dispase1 on ice and FACS sorted for CD31 and CD140b.
|
| Growth protocol |
Vascular organoids were cultured in DMEM:F12 (incl. Glutamax and NEAA) with 20%KOSR, 15%FBS, 100ng/ml VEGF and 100ng/mL FGF-2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA synthesis and amplification were performed from total RNA using SMARTer RNA Kit (Clontech) according to the manufacturers instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads mapping to human rRNA transcripts were removed using bwa/0.7.12 alignment and samtools/1.3.1. Remaining reads were aligned to human genome hg38 using TopHat v2.1.1 (GTF annotation file hg38, RefSeq from UCSC, 2015/01; library-type fr-unstranded). Reads in genes were counted with htseq-count v0.6.1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with per gene read counts
|
| |
|
| Submission date |
Jan 03, 2018 |
| Last update date |
Jan 01, 2020 |
| Contact name |
Reiner Wimmer |
| Organization name |
IMBA
|
| Street address |
Dr. Bohrgasse 3
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE108726 |
Vascular organoids differentiation from human induced pluripotent stem cells (iPSC) |
|
| Relations |
| BioSample |
SAMN08289287 |
| SRA |
SRX3529238 |
