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Status |
Public on Nov 10, 2021 |
Title |
P1CHIR2: Passage 1 CHIR-treated endothelial cells 2 |
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: CHIR differentiation (sample pairing): 2
|
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).
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|
|
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
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|
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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 |
SAMN18848546 |
SRA |
SRX10665588 |