|
| Status |
Public on Feb 06, 2024 |
| Title |
Con_48h_2 |
| Sample type |
RNA |
| |
|
| Source name |
Heart, exposed but unligated, 48h
|
| Organism |
Ciona intestinalis |
| Characteristics |
tissue: heart
injury: not injured
time point: 48h
|
| Treatment protocol |
Samples were prepared from control hearts (exposed but not ligated) or injured hearts (ligated or cryo injury) at 24h or 48h following treatment with two biological replicates per sample type. To set up ligations, hearts were exposed via a 3 cm incision in the animal’s tunic. Surgical silk (4 cm pieces of 000 gauge (Ethicon, NJ)) was tied around the exposed heart apex. Animals were placed in separate baskets for a 24- or 48-hour recovery period. At the end of each of these periods, hearts that were still visibly beating were processed for analysis. A minimum of 4 hearts per group was done for each experiment.
|
| Growth protocol |
Ciona intestinalis adults (7-12 cm) were obtained by M-REP (San Diego, CA). The animals were maintained in a 65-gallon saltwater tank equipped with appropriate water circulation and filtration system.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by RNeasy Mini Kit (Qiagen) from injured and control hearts at 24h or 48h following treatment.
|
| Label |
biotin
|
| Label protocol |
Total RNA (100 ng) was converted into biotin-labeled cRNA and then fragmented using the Affymetrix 3' IVT Express Kit in accordance with manufacturer protocols.
|
| |
|
| Hybridization protocol |
Targets (12.5 ug) were hybridized to Affymetrix Ciona intestinalis custom-designed array (CINT06a520380F - GPL15657) according to manufacturer protocols. Post hybridization washing and fluorescence labeling was done in an Affymetrix Fluidics Station 450 in accordance with manufacturer protocols.
|
| Scan protocol |
Microarrays were scanned using an Affymetrix 7G Scanner.
|
| Data processing |
CEL files imported into Affymetrix Expression Console software and processed with the custom annotation file and RMA.
|
| |
|
| Submission date |
Oct 05, 2023 |
| Last update date |
Feb 06, 2024 |
| Contact name |
Jeremy Barth |
| E-mail(s) |
barthj@musc.edu
|
| Organization name |
MUSC
|
| Street address |
173 Ashley Ave, BSB 627
|
| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
29425-5080 |
| Country |
USA |
| |
|
| Platform ID |
GPL15657 |
| Series (1) |
| GSE244713 |
Gene expression changes in injured myocardium of Ciona intestinalis |
|
