|
| Status |
Public on Dec 15, 2015 |
| Title |
Sample_KP33 |
| Sample type |
SRA |
| |
|
| Source name |
zebrafish epicardial cell
|
| Organism |
Danio rerio |
| Characteristics |
strain: EK
tissue: heart epicardium
age: 6 month
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ventricles were collected from adult tcf21:nucEGFP fish at 6 months of age. Ventricles were collected on ice and washed several times to remove blood cells. Ventricles were digested in an Eppendorf tube with 0.5 ml HBSS plus 0.13 U/ml Liberase DH (Roche) and 1% sheep serum at 37°C, while stirring gently with a Spinbar® magnetic stirring bar (Bel-Art Products). Supernatants were collected every 5 min and neutralized with sheep serum. Dissociated cells were spun down and re-suspended in DMEM plus 10% fetal bovine serum (FBS) medium with 1.5 μg/ml propidium iodide (PI), and sorted using a BD FACSVantage SE sorter for EGFP-positive and PI-negative cells. Single cells were captured using Fluidigm C1 platform. RNA extraction was done following the Fluidigm protocol.
Libraries were constructed on the C1 platform following the Fluidigm protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina CASAVA1.8 software used for basecalling.
Sequenced reads were mapped to the zebrafish genome using Bowtie2.
Transcript expressions were quantified by using RSEM 1.2.12
Genome_build: Zv9
Supplementary_files_format_and_content: Tab-delimited text files include expected count values for each sample.
|
| |
|
| Submission date |
Dec 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jingli Cao |
| E-mail(s) |
jic4001@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Cell & Developmental Biology
|
| Lab |
Jingli Cao
|
| Street address |
413 E 69th ST, BRB-518
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE75583 |
Single epicardial cell transcriptome sequencing identifies Caveolin-1 as an essential factor in zebrafish heart regeneration |
|
| Relations |
| BioSample |
SAMN04305349 |
| SRA |
SRX1457878 |
