|
| Status |
Public on Jan 30, 2019 |
| Title |
Left Ventricle_Replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
cardiomyocytes_Left Ventricle
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pediatric heart samples
tissue subtype: tissue samples of left ventricle
condition: tissue
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
IMR90 iPSCs were induced for cardiac differentiation using a growth factor-guided protocol. Cardiac spheres were generated from cells at differentiation day 5 and subjected to maturation factors or DMSO treatment from day 21 to day 28. RNA samples from cells at differentiation day 28 were prepared using Bio-Rad RNA extraction kit and 1 µg of total RNA/sample was used for the construction of sequencing libraries using Illumina TruSeq RNA Sample Prep Kit.
Libraries were generated using the Illumina standard TruSeq protocol and next-generation sequencing was done through an Illumina HiSeq 2500, 75bp paired end sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
DL_LV3_S6
Sample_6_LV3
|
| Data processing |
Reads were mapped to GRCh38 genome assembly with the HISAT2 followed by using UCSC reference annotation and HTSeq to estimate gene abundance.
Per sample read counts were calculated with htseq-count, mode: union, feature type: exon, id attribute: gene_id, and all other defaults.
Normalized read count abundance was estimated and differential expression was calculated with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).
|
| |
|
| Submission date |
Jan 29, 2019 |
| Last update date |
Feb 04, 2019 |
| Contact name |
Dong Li |
| E-mail(s) |
dli50@emory.edu
|
| Organization name |
Emory University
|
| Department |
Pediatrics
|
| Street address |
2015 UPPERGATE DR
|
| City |
ATLANTA |
| State/province |
GEORGIA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE125862 |
Gene expression profile in response to HIF-1α inhibition together with PPARα activation and the postnatal factors (T3, IGF-1 and dexamethasone) in hiPSC-CMs |
|
| Relations |
| BioSample |
SAMN10841537 |
| SRA |
SRX5307279 |
