|
| Status |
Public on Nov 30, 2023 |
| Title |
3dpa (6 rep) regeneration and 3dpa (6 rep) refractory |
| Sample type |
SRA |
| |
|
| Source name |
tail
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: tail
treatment: amputated
|
| Treatment protocol |
Amputation was performed manually (removal of ~30% of tail tissue) using tricaine anesthetized tadpoles at stage 40 (regenerative) and stage 46 (refractory). The tail was amputated after the following time periods: 1) regenerative 6 hpa and 1 dpa, 2) refractory 6 hpa and 1 dpa, 3) regenerative and refractory 3 dpa.
|
| Growth protocol |
Xenopus laevis females were stimulated with 500 U of human chorionic gonadotropin (Sigma-Aldrich). Eggs were collected the following day and fertilized by testes suspension which were surgically obtained from the male. After the removal of jelly coats by the 2% cysteine treatment, embryos were incubated in 0.1x MBS until the experimental procedure. Embryonic stages were determined based on Nieuwkoop and Faber table. Embryos were immediately transferred to the 0.1x MMR solution with gentamycin. Solution was changed every day.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Dissected tissues were embedded and oriented in 50% optimal cutting temperature (OCT) medium, rapidly frozen using dry ice and then transferred to -80°C for a maximum of six weeks of storage. Samples were sectioned sagitally (20 µm thickness) using Leica CM1950 cryostat (Leica Microsystems). Sections collected for the 10X Visium Spatial Gene Expression processing were then stored at -80°C.
Sequencing libraries were prepared according to the manufacturer’s manual “Visium Spatial Gene Expression Reagent Kits User Guide” (CG000239).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Spatial transcriptome sequencing
|
| Data processing |
Raw sequencing data were processed using the 10x Genomic Space Ranger function (v. 1.2.2)
Binary base call files were demultiplexed using mkfastq function with default parameters.
fastq files were mapped separately to Space ranger reference (XENLA_10.1_GCF) using count function which takes a microscope slide image and fastq files, performs alignment, tissue detection, fiducial detection, and barcode/UMI counting.
Spatial regeneration and refractory datasets were analyzed using Seurat (v. 5). Spots with greater than 20% reads for the mitochondrial genes were removed. Each dataset was normalized using SCTransform using vst.flavor v2.
Assembly: Xenopus laevis genome (v 10.1)
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv.gz: raw list of spatial barcodes
Supplementary files format and content: features.tsv.gz: raw list of gene IDs
Supplementary files format and content: matrix.mtx.gz: raw gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: processed_metadata.xlsx - metadata of the filtered and processed data, including the conditions and sample annotations used for downstream analysis
Library strategy: Spatial transcriptomics
|
| |
|
| Submission date |
Oct 13, 2023 |
| Last update date |
Nov 30, 2023 |
| Contact name |
Radek Sindelka |
| E-mail(s) |
Radek.Sindelka@ibt.cas.cz
|
| Organization name |
Institute of Biotechnology, Czech Academy of Science, v.v.i.
|
| Lab |
Laboratory of Gene Expression
|
| Street address |
Průmyslová 595
|
| City |
Vestec by Prague |
| ZIP/Postal code |
25250 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL28901 |
| Series (2) |
| GSE245313 |
Characterization of regeneration initiating cells during Xenopus laevis tail regeneration [spatial transcriptomics] |
| GSE245320 |
Characterization of regeneration initiating cells during Xenopus laevis tail regeneration |
|
| Relations |
| BioSample |
SAMN37805407 |
| SRA |
SRX22085456 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7840724_A1_frog_3dpa_barcodes.tsv.gz |
25.1 Kb |
(ftp)(http) |
TSV |
| GSM7840724_A1_frog_3dpa_detected_tissue_image.jpg.gz |
1.7 Mb |
(ftp)(http) |
JPG |
| GSM7840724_A1_frog_3dpa_features.tsv.gz |
318.1 Kb |
(ftp)(http) |
TSV |
| GSM7840724_A1_frog_3dpa_matrix.mtx.gz |
39.6 Mb |
(ftp)(http) |
MTX |
| GSM7840724_A1_frog_3dpa_processed_metadata.xlsx |
100.1 Kb |
(ftp)(http) |
XLSX |
| GSM7840724_A1_frog_3dpa_scalefactors_json.json.gz |
173 b |
(ftp)(http) |
JSON |
| GSM7840724_A1_frog_3dpa_tissue_hires_image.png.gz |
4.2 Mb |
(ftp)(http) |
PNG |
| GSM7840724_A1_frog_3dpa_tissue_lowres_image.png.gz |
406.7 Kb |
(ftp)(http) |
PNG |
| GSM7840724_A1_frog_3dpa_tissue_positions_list.csv.gz |
64.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
