|
| Status |
Public on Aug 24, 2024 |
| Title |
NovaST_coronal_section_plate5 |
| Sample type |
SRA |
| |
|
| Source name |
Telencephalon
|
| Organism |
Gallus gallus |
| Characteristics |
tissue: Telencephalon
breed: broiler
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Telencephalons from 15 days old domestic chickens were dissected and immediately snap-frozen in isopentane for 10 min. Afterwards, the telencephalon was embedded in Tissue-Tek OCT cryo embedding compound, 10μm sections were cut using a cryostat and placed on Nova-ST chips
Pepsin was used to permeabilise the sectioned tissue and Maxima Rtase for the reverse transcription. Samples were treated with endonuclease and then tissue was cleared with Proteinase K. Klenow Fragment was used for second strand synthesis and the resulting cDNA was amplified and prepared for sequencing by addition of indexes and Illumina flow cell attachment sites.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Description |
Fresh frozen Nova-ST spatial transcriptome sequencing
|
| Data processing |
Raw sequencing data was processed using bcl2fastq to generate fastq files
Nova-ST chip tiles were identified using a subset of data, and a witelist of barcodes was created from these tiles. Data was mapped and quantified against the mm10 using this whitelist and STARsolo
X/Y coordinates for barcodes with identified counts were normalised into a chip-based space and used alongside the expression data to create GEM files.
Assembly: galGal6
Supplementary files format and content: tif: H&E stained images
Supplementary files format and content: gem.gz: GEM formatted expression matrix including normalized X/Y coordinates of each cluster
Supplementary files format and content: BC_Coords.pickle: Python pickled dictionaries containing barcodes, tile information and X/Y coordinates used for whitelist creation.
Library strategy: Spatial Transcriptomics (Nova-ST)
|
| |
|
| Submission date |
Aug 17, 2024 |
| Last update date |
Aug 24, 2024 |
| Contact name |
Stein Aerts |
| E-mail(s) |
stein.aerts@kuleuven.be
|
| Organization name |
VIB-KU Leuven
|
| Department |
Center for Brain and Disease Research
|
| Lab |
Laboratory of Computational Biology
|
| Street address |
Herestraat 49 PO Box 602
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL34823 |
| Series (1) |
| GSE275097 |
Enhancer-driven cell type comparison reveals similarities between the mammalian and avian telencephalon |
|
| Relations |
| BioSample |
SAMN43239710 |
| SRA |
SRX25742393 |
