|
| Status |
Public on Jul 12, 2024 |
| Title |
biol rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Distal tibia fracture callus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Distal tibia fracture callus
genotype: Nf1[+/flox] and Postn-cre;Nf1[flox/-]
treatment: 10-day post-surgery
|
| Treatment protocol |
Distal tibia fractures were introduced into adult mice. Ten days after fracture, calluses were dissected, fixed in formallin, and decalicified in 14% EDTA for 3 days prior to embedding.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10X Genomics Visium mouse FFPE
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X Genomics Visium FFPE
|
| Data processing |
Raw sequence files were analysed by SpaceRanger software (v1.3.0) with reads mapped to mouse reference mm39.
Assembly: mm39
Supplementary files format and content: H5 files were generated for each sample following mapping by SpaceRanger.
Supplementary files format and content: Matrix files were generated for each sample following mapping by SpaceRanger.
Supplementary files format and content: JPEG files are provided for H/E stained sections for each sample matching the Visium fiduciary window.
Supplementary files format and content: aligned_fiducials.jpg: Fiducial alignment image
Supplementary files format and content: detected_tissue_image.jpg: Detected tissue image
Supplementary files format and content: scalefactors_json.json: Scale factor json file
Supplementary files format and content: tissue_hires_image.png: high resolution H/E image
Supplementary files format and content: tissue_lowres_image.png: low resolution H/E image
Supplementary files format and content: tissue_positions_list.csv: barcode position file
Supplementary files format and content: filtered_feature_bc_matrix.h5: filter feature h5 file
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Nov 15, 2022 |
| Last update date |
Jul 24, 2024 |
| Contact name |
Jonathan Rios |
| E-mail(s) |
jonathan.rios@tsrh.org
|
| Organization name |
Scottish Rite for Children
|
| Street address |
2222 Welborn Street
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75219 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE218046 |
Spatial transcriptomic analysis of a pre-clinical NF1 pseudarthrosis fracture model |
|
| Relations |
| BioSample |
SAMN31743351 |
| SRA |
SRX18276204 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6733377_C1_CKDL220014177-1A_HY5MFDSX3_S2.h5 |
8.9 Mb |
(ftp)(http) |
H5 |
| GSM6733377_C1_CKDL220014177-1A_HY5MFDSX3_S2.jpg.gz |
226.2 Mb |
(ftp)(http) |
JPG |
| GSM6733377_C1_CKDL220014177-1A_HY5MFDSX3_S2.txt.gz |
8.0 Mb |
(ftp)(http) |
TXT |
| GSM6733377_C1_CKDL220014177-1A_HY5MFDSX3_S2_Genotype_annotations.txt.gz |
19.9 Kb |
(ftp)(http) |
TXT |
| GSM6733377_aligned_fiducials.jpg.gz |
1.5 Mb |
(ftp)(http) |
JPG |
| GSM6733377_detected_tissue_image.jpg.gz |
1.7 Mb |
(ftp)(http) |
JPG |
| GSM6733377_filtered_feature_bc_matrix.h5 |
8.9 Mb |
(ftp)(http) |
H5 |
| GSM6733377_scalefactors_json.json.gz |
167 b |
(ftp)(http) |
JSON |
| GSM6733377_tissue_hires_image.png.gz |
10.0 Mb |
(ftp)(http) |
PNG |
| GSM6733377_tissue_lowres_image.png.gz |
936.8 Kb |
(ftp)(http) |
PNG |
| GSM6733377_tissue_positions_list.csv.gz |
58.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
