|
| Status |
Public on Mar 20, 2024 |
| Title |
H3KO_4 |
| Sample type |
SRA |
| |
|
| Source name |
Total heart cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Total heart cells
strain: C57BL/6
age: E11.5
genotype: Hdac3f/f; Tie2-Cre/+; R26eYFP/+
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| 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 |
GPL19057 |
| Series (2) |
| GSE229660 |
Endocardial HDAC3 is required for myocardial trabeculation [single-cell RNA-seq] |
| GSE229661 |
Endocardial HDAC3 is required for myocardial trabeculation |
|
| Relations |
| SRA |
SRX19960905 |
| BioSample |
SAMN34174474 |
