|
| Status |
Public on Apr 28, 2023 |
| Title |
acomys PD |
| Sample type |
SRA |
| |
|
| Source name |
ear pinna skin
|
| Organism |
Acomys cahirinus |
| Characteristics |
tissue: healing ear punch
strain: wild-type
treatment: ERK inhibitor
|
| Treatment protocol |
pERK, FGFR and ErbB2 inhibitors were injected from D12 to D15, similarly to DMSO control; micro-beads soaked with either PBS, recombinant FGF-2/NRG-1 were implanted locally at D10.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tissue was dissociated into single cell suspension using Protease from B. Licheniformis and Dounce homogenizer. Red blood cells were removed with RBC lysis buffer. Centrifugation steps were performed at 300g 5min. Cells were resuspended in PBS/BSA 0.04%
The barcoding of individual transcripts from single cells, followed by cDNA amplification and library construction, were performed using 10X Genomics reagents and 10X Chromium Controller, according to the manufacturer’s user guide nr. CG000315 (“Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index), RevC”).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
LX055
|
| Data processing |
10x genomics cellranger version 6.1.1 was used for all the analysis steps from fastq.gz to count tables
Assembly: For the mouse samples, the 10x genomics genome refdata-gex-mm10-2020-A (which is Mus musculus, GRCm38, patchlevel 6 and gencode version M23). For the Acomys samples, a custom genome was used.
Supplementary files format and content: 10x genomics cellranger 6.1.1 hdf5 file. For details see https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices
|
| |
|
| Submission date |
Feb 03, 2023 |
| Last update date |
Apr 29, 2023 |
| Contact name |
PHILIP LIJNZAAD |
| E-mail(s) |
p.lijnzaad@prinsesmaximacentrum.nl
|
| Organization name |
Princess Maxima Center for Pediatric Oncology
|
| Department |
Single Cell Facility
|
| Lab |
Holstege Lab
|
| Street address |
HEIDELBERGLAAN 25
|
| City |
UTRECHT |
| State/province |
Utrecht |
| ZIP/Postal code |
3584 CS |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL29848 |
| Series (1) |
| GSE224433 |
An ERK-dependent molecular switch antagonizes fibrosis and promotes regeneration in spiny mice (Acomys) |
|
| Relations |
| BioSample |
SAMN33052328 |
| SRA |
SRX19272769 |
