|
| Status |
Public on Aug 28, 2018 |
| Title |
C15_day6_C_1 (RNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
hiPSC-derived cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: hiPSC-derived cells
cell line: C15
treatment: Control
differentiation time (days): 6
|
| 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 was extracted using miRNeasy Mini Kit (Qiagen), and RNA was then subjected to DNase I digestion and purified using a RNeasy Mini spin column (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. . All RNA-seq libraries were sequenced by HiSeq 4000 sequencers (Illumina) with 2 x 101 cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| 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.
The human gene symbols and their raw counts were calculated using HTSeq (version 0.6.1p1) package in Python with GRCh39/hg19 Homo sapiens gtf file.
Differential gene-expression analysis was performed using edgeR package in R, and the normalization was performed using a trimmed mean of M-values (TMM)method.
Genome_build: hg19
Supplementary_files_format_and_content: fastq
|
| |
|
| Submission date |
Aug 20, 2016 |
| Last update date |
Oct 11, 2022 |
| Contact name |
Qing Liu |
| E-mail(s) |
liuqingcell@gmail.com
|
| 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 |
GPL20301 |
| Series (2) |
| GSE85880 |
Genome-wide transcriptomic profiling of cardiomyocyte differentiation from human ES cells and iPS cells under exposure to sublethal of isotretinoin (RNA-seq) |
| GSE85881 |
ES cells and iPS cells under exposure to sublethal of isotretinoin |
|
| Relations |
| BioSample |
SAMN05601421 |
| SRA |
SRX2036775 |
