|
| Status |
Public on Feb 17, 2021 |
| Title |
IRX4-8-1-p2-2A |
| Sample type |
SRA |
| |
|
| Source name |
iPSC-derived cardiac myocytes
|
| Organism |
Homo sapiens |
| Characteristics |
celltype: iPSC-derived cardiac myocytes
cell line: WTc
sirna target: IRX4
replicate number: 1
treatment type: targeting siRNA
|
| Treatment protocol |
Oligos for siRNA knockdown were ordered from Horizon Discovery. A total of three oligos per target were pooled together. All knockdown experiments were performed in triplicate. Knockdown (day 0) was performed using the Lipofectamine RNAiMAX reagent (ThermoFisher) and pooled siRNA at a final concentration of 10uM. Media was changed to fresh media 48 hours later. Five days post knockdown, a second identical dose of lipofectamine+siRNA was added to the cells for another 48 hours
|
| Growth protocol |
Cardiac myocytes were obtained by differentiating human induced pluripotent stem cells (WTc cell line) as described previously (Miyaoka et al. 2014; Judge et al. 2017).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells lysed with buffer RLT on Day 10 after first transfection. RNA extraction by Qiagen RNeasy kit.
NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490L), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB E7770L), NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB E7600S)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Base-calling performed by Illumina Basespace
Alignment to hg19 performed by STAR v2.5.2a
Gene-level counts quantified by HTSeq v0.6.1 with settings --mode=union \ --stranded=no \ --type=exon \ --order=name Genome_build: hg19
Supplementary_files_format_and_content: gene-level counts per sample were generated using HTSeq
|
| |
|
| Submission date |
Feb 16, 2021 |
| Last update date |
Feb 17, 2021 |
| Contact name |
Ian A Mellis |
| E-mail(s) |
[email protected]
|
| Organization name |
Columbia University
|
| Street address |
622 W 168th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE166823 |
Gene expression after knockdown of transcription factors in human iPSC-derived cardiac myocytes |
|
| Relations |
| BioSample |
SAMN17924446 |
| SRA |
SRX10108220 |
