|
| Status |
Public on Jul 03, 2019 |
| Title |
RNA-seq_IV-1-MT, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-CMs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: iPSC-CMs
day post-differentiation: day 40
genotype/variation: LMNAT WT/Ins-MT
|
| Treatment protocol |
iPSCs were grown to 90% confluence and subsequently differentiated into beating cardiomyocytes, using a small-molecule-based monolayer method described previously. Ten days after cardiac differentiation, iPSC-CM monolayers were purified using RPMI-1640 without glucose (Life Technologies) with B27 supplement (Life Technologies). Non-glucose culture medium was changed every 2 days. After 5 days, iPSC-CMs were reseeded onto Matrigel-coated plates in a culture medium containing glucose.
|
| Growth protocol |
iPSC lines were maintained in chemically defined medium Essential 8 (E8 medium) (Life Technologies) on Matrigel-coated (BD Bioscience, San Jose, CA) plates at 37°C with 5% (vol/vol) CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
iPSC-CMs were detached from cell culture plates and RNA was extracted using a microRNeasy kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
Isogenic line of IV-1 to insert LMNA mutation (heterozygous line)
RNA-seq Replicate #1
|
| Data processing |
Base quality of raw reads: FastQC 0.11.4
Aligned the reads to the human reference genome (hg19): STAR 2.5.1b
Calculating fragments per kilobase per million aligned reads (FPKM): Cufflinks 2.2.1
Genome_build: human reference genome hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Aug 21, 2018 |
| Last update date |
Jul 03, 2019 |
| Contact name |
Lei Tian |
| E-mail(s) |
tianlei@stanford.edu
|
| Phone |
6502388262
|
| Organization name |
Stanford's Postdoctoral Scholar programs
|
| Street address |
1215 Welch Rd
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (2) |
| GSE118882 |
Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy [RNA-seq] |
| GSE118885 |
Dysregulation of PDGFRB contributes to the pathogenesis of LMNA-related dilated cardiomyopathy |
|
| Relations |
| BioSample |
SAMN09873822 |
| SRA |
SRX4590590 |
