|
| Status |
Public on Mar 20, 2024 |
| Title |
Bulk RNA_Mouse Cardiac Endothelial Cell - Hdac3 Crispr/cas9 Knockout (KO) - rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Cardiac Endothelial Cell
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse Cardiac Endothelial Cell
cell line: Mouse Cardiac Endothelial Cells
genotype: Hdac3 knockout
treatment: Hdac3 sgRNA lentivirus transduction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 2 ug of RNA was used for the construction of sequencing libraries.
llumina standard protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw image data file from high-throughput sequencing was transformed to Sequenced Reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality.
For the samples with biological replicates: Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.6.3). The padj<0.05 was set as the threshold for significantly differential expression by default
Assembly: mm10
|
| |
|
| Submission date |
Apr 13, 2023 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Deqiang Li |
| Organization name |
Nationwide Children's Hospital
|
| Lab |
Li Lab
|
| Street address |
575 Children’s Crossroad, WB4321
|
| City |
COLUMBUS |
| State/province |
Ohio |
| ZIP/Postal code |
43215 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE229661 |
Endocardial HDAC3 is required for myocardial trabeculation |
| GSE229677 |
Endocardial HDAC3 is required for myocardial trabeculation [bulk RNA-seq] |
|
| Relations |
| SRA |
SRX19961092 |
| BioSample |
SAMN34174818 |
