|
| Status |
Public on Apr 26, 2019 |
| Title |
1001D0_2 |
| Sample type |
SRA |
| |
|
| Source name |
HS1001 from Dr. Hovatta’s laboratory (Rodin et al., 2014)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human embryonic stem cells
cell line: HS1001
biological replicate: 2
time: day 0
|
| Treatment protocol |
At day 0, medium was supplemented with 10 mg of CHIR99021 and at day 3, medium was supplemented with 5 mg IWP2
|
| Growth protocol |
Cells were cultured in triplicates wells coated with LN-521 and LN-221. Cells at day 0 were cultured with Nutristem medium. Cells at Day 1 and 3 were cultured in RMPI 1640 with B27 without insulin supplement and CHIR99021. Cells at day 5 were cultured in RMPI 1640 with B27 without insulin supplement and IWP2. Cells at day 7 and 9 were cultured in RMPI 1640 with B27 without insulin supplement. Cells at day 11 to 90 were cultured in RPMI 1640 supplemented with CTS B-27 Supplement.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with Norgen Biotek's Single-cell RNA-isolation kit according to manufacturer's protocol. 700 ng of total RNA was used for library construction.
Libraries were constructed with TruSeq stranded total RNA library Prep Kit (Illumina).
Samples were multiplexed with 10 samples per lane and sequenced in Illumina HiSeq 3000 RNA sequencing platform (150bp pair-end reads)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Cells maintained on LN-521+LN-221
|
| Data processing |
All reads were assessed for quality and (when necessary) adaptors were removed using Cutadapt.
RNA-Seq reads were aligned to hg38 (Ensembl Gene annotation build 79) using STAR 2.5.2b
Reads were quantified using RSEM 1.2.31
Genome_build: hg38 (Ensembl Gene annotation build 79)
Supplementary_files_format_and_content: HS1001_timecourse_TPM.txt: tab separated file with TPM values for each gene and sample; HS1001_timecourse_gene_raw_counts.txt: tab separated file with raw gene expression counts for each gene and sample
|
| |
|
| Submission date |
Jul 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Aida Moreno-Moral |
| Organization name |
Duke-NUS Medical School
|
| Street address |
8 College Road
|
| City |
Singapore |
| ZIP/Postal code |
169857 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE100722 |
In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors [HS1001 differentiation protocol] |
| GSE100725 |
In vivo generation of post-infarct human cardiac muscle by laminin-promoted cardiovascular progenitors |
|
| Relations |
| BioSample |
SAMN07311832 |
| SRA |
SRX2978659 |
