|
| Status |
Public on Jun 30, 2023 |
| Title |
H1_Day3_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
H1_Day3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H1
cell type: human embryonic stem cells (hESCs)
genotype/variation: Wild type
differentiation time: Day3
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the NucleoZol reagent and quantified by NanoDrop spectrophotometer.
mRNA libraries were prepared using the VAHTS® mRNA-seq V2 Library Prep Kit for Illumina from Vazyme protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
Raw RNA-seq sequenced reads were quality tested using FASTQC
Data were aligned to GRCh38/hg38 Homo sapiens reference genome using STAR aligner with ENCODE standard options for long RNA-seq pipeline
RSEM was used to estimate gene expression abundance and calculate TPM values
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Nov 04, 2021 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Weisheng Cheng |
| E-mail(s) |
chengwsh@outlook.com
|
| Organization name |
Sun yat-sen University
|
| Street address |
2nd Zhongshan Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE188111 |
Genome-wide transcriptomic profiling of cardiomyocyte differentiation from Wild-type and PERK-KO H1 hESCs [RNA-seq] |
| GSE188123 |
RNA-seq and ChIP-seq studies of cardiomyocyte differentiation from H1 hESCs |
|
| Relations |
| BioSample |
SAMN22876555 |
| SRA |
SRX12968575 |
