|
| Status |
Public on Jul 12, 2024 |
| Title |
KO2 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
strain: C57BL6/J
genotype: Sema6d-/-
age: 6-8 weeks old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse brain slide gene expression were detected by 10x Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared for sequencing using 10x Visium spatial protocols and standard Illumina protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
GA46632
|
| Data processing |
library strategy: Visium spatial transcriptomics
Sequencing was performed on NovaSeq 6000 platform in a 28+90-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Raw sequencing data for each sample were converted to matrices of expression using Space Ranger (version spaceranger-1.3.0, 10X Genomics).
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcode
Supplementary files format and content: features.tsv.gz: list of gene name and Ensembl ID
Supplementary files format and content: matrix.mtx.gz: non-zero gene expresion count data in Matrix Market Exchange Formats
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcode and the cordinate specifying spot
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: tissue_hires_image.png: image of tissue
Supplementary files format and content: filtered_feature_bc_matrix.h5 : HDF5 format files including counts data for each gene and spot-position (barcode) combination
Supplementary files format and content: spatial.zip : zipped "spatial" foler which is one of output folders of Space Ranger software (10X genomics)
|
| |
|
| Submission date |
Dec 13, 2022 |
| Last update date |
Jul 12, 2024 |
| Contact name |
Daisuke Motooka |
| E-mail(s) |
dry_team@ngs.gen-info.osaka-u.ac.jp
|
| Organization name |
NGS core facility, Research Institute for Microbial Diseases, Osaka University
|
| Street address |
3-1, Yamadaoka
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE220799 |
Spatial gene expression profile of the brain from WT and Sema6d-/- mice |
|
| Relations |
| BioSample |
SAMN32187132 |
| SRA |
SRX18665935 |
