|
| Status |
Public on Jul 10, 2017 |
| Title |
H9_4_1_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
hESC-derived cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hESC-derived cells
cell line: H9
differentiation time (days): 4
|
| Treatment protocol |
The cardiomyocyte differentiation was initiated using a monolayer differentiation method with PSC Cardiomyocyte Differentiation kit (Thermo Fisher Scientific).
|
| Growth protocol |
Both hESCs and hiPSCs were grown in Matrigel (Corning)-coated 12-well plates with Essential 8™ Medium (Thermo Fisher Scientific).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from approximately 3-5 million cells were extracted using QIAzol lysis ralleagent (QIAGEN), and then were subjected to DNase I digestion and purified by AllPrep DNA/RNA Mini Kit (QIAGEN) according to the manufacturer’s instructions.
RNA-seq libraries were constructed using ScriptSeq™ v2 RNA-Seq Library Preparation kit (Epicentre Biotechnologies) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
biological replicate 1
|
| Data processing |
RNA-seq fastq data were aligned with Tophat (version 2.0.9) to GRCh39/hg19 Homo sapiens reference genome from the UCSC Genome Browser.
Cuffdiff of the Cufflinks software (version 2.2.1) and GRCh39/hg19 Homo sapiens gtf file from UCSC Genome Browser were used to estimate abundances of transcripts and generate their FPKM values.
Table of FPKM values of all samples were created using cummeRbund package in R.
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM values.
|
| |
|
| Submission date |
Aug 08, 2016 |
| Last update date |
Oct 11, 2022 |
| Contact name |
Qing Liu |
| E-mail(s) |
[email protected]
|
| Organization name |
Clemson University
|
| Department |
Biological Sciences
|
| Lab |
Qing Liu
|
| Street address |
Jordan Hall
|
| City |
Clemson |
| State/province |
SC |
| ZIP/Postal code |
29634 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE85331 |
Genome-wide transcriptomic analysis of cardiomyocyte differentiation from human embryonic stem cells and iPS cells (RNA-seq) |
| GSE85332 |
Genome-wide transcriptomic analysis and chromatin accessibility profiling of cardiomyocyte differentiation from human embryonic stem cells and iPS cells |
|
| Relations |
| BioSample |
SAMN05525610 |
| SRA |
SRX2008133 |
