|
| Status |
Public on Mar 04, 2022 |
| Title |
Sample 12: control knockdown rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
human iPS cell derived cardiomyocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WTC-11
cell type: human induced pluripotent stem cell derived cardiomyocytes (iPSCs)
genotype/variation: control knockdown
|
| Treatment protocol |
LINC000881 knockdown was achieved by lipofectamine based transfection of antisense LNA GapmeRs designed against LINC00881 versus scrambled oligonucleotide. LINC000881 overexpression was achieved by lipofectamine based transfection of LINC00881 plasmid versus bacterial alkaline phosphatase control plasmid.
|
| Growth protocol |
iPSCs were maintained in RPMI 1640 with B27 supplement. Experiments were performed using cells at day 15 - 35.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy kit was used to isolate RNA following manufacturer's guidelines. DNAse digestion on column was performed.
Sequencing libraries were constructed using the TruSeq Stranded Total RNA Library Prep Gold mRNA (Illumina, San Diego CA) with an input of 1000ng and 11 cycles final amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample 12 - (VX20217)
|
| Data processing |
Read alignment performed using the splice-aware aligner STAR v.2.7.3a
Genome_build: Gencode v38
|
| |
|
| Submission date |
Mar 01, 2022 |
| Last update date |
Mar 04, 2022 |
| Contact name |
Veli K Topkara |
| E-mail(s) |
vt2113@cumc.columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Cardiology
|
| Lab |
Topkara Lab
|
| Street address |
622W 168th St, PH10-203A
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE197671 |
Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading Identifies LINC00881 as an Essential Regulator of Calcium Handling in the Cardiomyocyte [RNAseq] |
| GSE197672 |
Genome-Wide DNA Methylation Profiling of the Failing Human Heart with Mechanical Unloading Identifies LINC00881 as an Essential Regulator of Calcium Handling in the Cardiomyocyte |
|
| Relations |
| BioSample |
SAMN26343515 |
| SRA |
SRX14330870 |
