|
| Status |
Public on Apr 27, 2023 |
| Title |
ChickTrunk_4_Visium |
| Sample type |
SRA |
| |
|
| Source name |
embryonic trunk
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: embryonic trunk
cell type: tissue
breed: white leghorn
genotype: wild-type
|
| Treatment protocol |
none; unlabeled, wild-type tissue
|
| Growth protocol |
See PMID: 36840366 (DOI: 10.1002/dvdy.577) methods
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The Visium Spatial Gene Expression Slide PN-2000233 and associated protocol (CG000239) from 10X Genomics were used. Fresh frozen HH24 trunk tissues were transversely cryo-sectioned to approximate single cell thickness (10um) and carefully placed within the fiducial frame on the equilibrated slide within a cryostat set to -20C. The slide was fixed in methanol at -20C for 30 min and air dried. The slide was then stained with H&E and imaged using a Zeiss LSM 800 confocal microscope. Tissue was permeabilized to release mRNA that bound to spatially barcoded capture probes.
Library preparation was done following the Visium Spatial Gene Expression User Guide using supplied reagents in Visium kit (10X Genomics).
Whole transcriptome libraries were sequenced and analyzed using Space Ranger (1.0.0) and Loupe browser. 10X Genomics‘ automated image alignment software had trouble detecting one capture area and we manually selected it in its Loupe browser based on 10X’s suggestion. Data was generated for four individual Visium capture areas.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Visium data was analyzed using Loupe cell browser from 10x Genomics, manually selecting the entire capture area. Data was processed using spaceranger 1.0.0 from 10x Genomics.
Data was aligned to the galGal6 chicken genome from UCSC using annotations from Ensembl 98. Data was aligned with STAR 2.5.1b as part of the spaceranger pipeline.
After spaceranger, data was analyzed in R 3.6.1 using Seurat 3.1.2. Spots were kept with > 10 counts per spot. Sctransform in Seurat was used for normalization.
Assembly: galGal6
Supplementary files format and content: *_barcodes.tsv.gz - output from spaceranger containing the barcodes from the visium experiment
Supplementary files format and content: *_features.tsv.gz - output from spaceranger containing the features (genes) from the visium experiment
Supplementary files format and content: *_matrix.mtx.gz - output from spaceranger containing the gene by spot matrix
Supplementary files format and content: rds file for each of four capture areas on visium slide - serialized R data file containing a Seurat object.
Library strategy: spatial transcriptomics
|
| |
|
| Submission date |
Apr 27, 2023 |
| Last update date |
Apr 27, 2023 |
| Contact name |
Madelaine Gogol |
| Organization name |
Stowers Institute
|
| Department |
Computational Biology Core
|
| Street address |
1000 E. 50th Street
|
| City |
Kansas City |
| State/province |
MO |
| ZIP/Postal code |
64110 |
| Country |
USA |
| |
|
| Platform ID |
GPL19787 |
| Series (2) |
| GSE230778 |
Cell-Type Profiling of the Sympathetic Nervous System Using Spatial Transcriptomics and Spatial Mapping of mRNA [Spatial Transcriptomics] |
| GSE230780 |
Cell-Type Profiling of the Sympathetic Nervous System Using Spatial Transcriptomics and Spatial Mapping of mRNA |
|
| Relations |
| BioSample |
SAMN34406816 |
| SRA |
SRX20119536 |
