|
| Status |
Public on Feb 22, 2024 |
| Title |
Nova-ST_MouseBrain_Rep4 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
genotype: C57BL/6J
|
| Growth protocol |
Six to eight weeks old mice (C57BL/6J) used in the study were kept on a 14 h light, 10 h dark–light cycle from 7:00 to 21:00
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Brains were dissected and immediately snap-frozen in isopentane for 10 min. Afterwards, brains were embedded in Tissue-Tek OCT cryo embedding compound, 10μm sections were cut using a cryostat and placed on the 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 |
NextSeq 2000 |
| |
|
| 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: mm10
Supplementary files format and content: tiff: H&E stained images
Supplementary files format and content: gem.txt.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 |
Feb 22, 2024 |
| Last update date |
Feb 22, 2024 |
| Contact name |
Kristofer James Davie |
| Organization name |
Vlaams Instituut voor Biotechnologie
|
| Department |
Center for Brain and Disease Research
|
| Street address |
Herestraat 49
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE256318 |
Nova-ST: Nano-Patterned Ultra-Dense platform for spatial transcriptomics [Nova-ST] |
|
| Relations |
| BioSample |
SAMN40033883 |
| SRA |
SRX23699082 |
