|
| Status |
Public on Nov 10, 2021 |
| Title |
P1DMSO3: Passage 1 DMSO-treated endothelial cells 3 |
| Sample type |
SRA |
| |
|
| Source name |
Human induced pluripotent stem cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: iPS(IMR90)-4
cell type: endothelial cells
passage number: 1
treatment: DMSO
differentiation (sample pairing): 3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed using Buffer RLT (Qiagen) supplemented with 1% beta-mercaptoethanol. RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) according to manufacturer instructions.
First-strand cDNA synthesis (with polyA enrichment) was performed using the SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio), followed by 9 cycles of PCR amplification. Libraries were prepared using the Nextera XT DNA Library Prep Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalling was performed by the Illumina NovaSeq 6000
FASTQ files were aligned and transcripts quantified using RSEM (v1.3.3) calling bowtie2 (v2.4.2)
Genome_build: hg38
Supplementary_files_format_and_content: An Excel spreadsheet containing raw counts and TPM values is provided
|
| |
|
| Submission date |
Apr 23, 2021 |
| Last update date |
Nov 10, 2021 |
| Contact name |
Benjamin D Gastfriend |
| Organization name |
University of Wisconsin-Madison
|
| Street address |
1415 Engineering Drive
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE173206 |
RNA-sequencing of human pluripotent stem-cell derived endothelial cells under control and Wnt-activating conditions |
|
| Relations |
| BioSample |
SAMN18848549 |
| SRA |
SRX10665585 |
