|
| Status |
Public on Jun 07, 2023 |
| Title |
mouse brain coronal tissue section 3, PCI |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
genotype: C57BL/6J
treatment: PCI
|
| Treatment protocol |
Improved immunostaining protocol presented in the accompanying publication Hahn et al.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
According to Visium Spatial Gene Expression User Guide (CG000239, Rev E).
Tissue permeabilization time: 8 min. After transfer of cDNA from slide, cDNA was amplified with 14 cycles and after adapter ligation, sample index PCR was performed in dependence of the sample with 16 to 17 cycles.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
bcl2fastq v2.20.0.422
spaceranger count (spaceranger-1.3.1)
spaceranger mat2csv (spaceranger-1.3.1)
Assembly: Mouse reference, mm10 (GENCODE vM23/Ensembl 98); pre-build for Cell Ranger (2020-A)
Supplementary files format and content: Tagged Image File Format
Supplementary files format and content: filtered feature-barcode matrix
Library strategy: 10X Visium Spatial Transcriptomics
|
| |
|
| Submission date |
Apr 03, 2023 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Marco Groth |
| E-mail(s) |
cfngs@leibniz-fli.de
|
| Organization name |
Leibniz Institute on Aging - FLI
|
| Department |
Core Facility - Next Generation Sequencing
|
| Street address |
Beutenbergstraße 11
|
| City |
Jena |
| ZIP/Postal code |
07747 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE228891 |
Protecting RNA Integrity for Spatial Transcriptomics While Improving Immunofluorescent Staining Quality |
|
| Relations |
| BioSample |
SAMN34062216 |
| SRA |
SRX19859607 |
