|
| Status |
Public on Jan 26, 2018 |
| Title |
VSMC-Alginate hydrogel-d6-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Vascular smooth muscle cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hESC-derived vascular smooth muscle cells
initial cell type: hESC-H9(WA09)
culture system: alginate hydrogel
|
| Growth protocol |
H9s were maintained in E8 medium for routine culture. Then H9s were differentiated into ECs, NSCs and VSMCs in 2D, 3D PEG hydrogel and alginate hydrogel cell culture system according to their differentiation protocol. mRNAs were sequenced.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested after differentiation and total RNA was isolated with RNAeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNAse treatment was performed to remove genomic DNA contamination (Qiagen).
Libraries were prepared using TruSeq RNA v2 library preparation reagents. 15 samples including ECs and NSCs were sequenced one lane and the rest samples were sequenced another lane.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to rice genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each gene with htseq-count
Genome_build: Human genome GRC37/Hg19
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts
|
| |
|
| Submission date |
Jan 25, 2018 |
| Last update date |
Jan 26, 2018 |
| Contact name |
Chi Zhang |
| E-mail(s) |
czhang5@unl.edu
|
| Organization name |
University of Nebraska - Lincoln
|
| Street address |
1901 Vine Street
|
| City |
Lincoln |
| State/province |
NE |
| ZIP/Postal code |
68588 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE109683 |
Differential gene expressions of human pluripotent stem cells derived cells in different culture system |
|
| Relations |
| BioSample |
SAMN08397729 |
| SRA |
SRX3601312 |
