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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 10, 2025 |
| Title |
g-Sox9+Trps1 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
strain: R26-Cas9-Fezh
Sex: male
age: 12-16 weeks old
timepoint: 7dpi
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| Treatment protocol |
The animals were injected with the Mok-LV virus for CRISPR mediated deletion of Sox9, Trps1 (or control)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse brains were embedded and snap frozen in an isopentane/liquid nitrogen bath. Two coronal sections (10µm) of the dorsal brain area were collected in each capture area and the tissue was enzymatically permeabelized according to the Visium Spatial Gene Expression from 10x Genomics.
Library was performed according to the manufacter’s instructions (Visium Spatial Gene Expression , 10x Genomics).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
10x Genomics, Visium Spatial Gene Expression, spaceranger v1.2.2
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| Data processing |
Data demultiplexing was performed using the Je tool v1.2
Alignment was performed using Space Ranger v1.2.2
Tissue_hires_image.png images of brain sections were acquired on a Carl Zeiss Axio Imager.M2m microscope
In all the samples, only one of the two coronal sections used had sufficient reads (possibly due to a technical artefact during tissue processing or sequencing). The spots corresponding to the tissue with good reads were subsetted and subsequent analysis was performed.
gRNA_injection.tiff images of brain sections were acquired on a Carl Zeiss Axio Imager.M2m microscope. This was used to define the injection region.
Assembly: mm10
Supplementary files format and content: barcode.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5,: Tab-separated values files and matrix files
Supplementary files format and content: tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg: image files
Library strategy: Spatial transcriptomics
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| Submission date |
Oct 17, 2024 |
| Last update date |
Feb 10, 2025 |
| Contact name |
Giacomo Masserdotti |
| E-mail(s) |
giacomo.masserdotti@helmholtz-munich.de
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| Organization name |
Helmholtz Zentrum
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| Department |
ISF
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| Street address |
Groshaderner Strasse 9
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| City |
Planegg-Martinstied |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE279676 |
Single cell deletion of the transcription factors Sox9 and Trps1 reveals novel functions in adult cortical astrocytes [Spatial transcriptomics] |
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| Relations |
| BioSample |
SAMN44326674 |
| SRA |
SRX26410878 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8577747_Cond4_1_gRNA_injection.tiff.gz |
8.1 Mb |
(ftp)(http) |
TIFF |
| GSM8577747_Cond4_2_gRNA_injection.tiff.gz |
7.9 Mb |
(ftp)(http) |
TIFF |
| GSM8577747_Cond4_aligned_fiducials.jpg.gz |
1.3 Mb |
(ftp)(http) |
JPG |
| GSM8577747_Cond4_barcodes.tsv.gz |
12.4 Kb |
(ftp)(http) |
TSV |
| GSM8577747_Cond4_detected_tissue_image.jpg.gz |
1.7 Mb |
(ftp)(http) |
JPG |
| GSM8577747_Cond4_features.tsv.gz |
209.9 Kb |
(ftp)(http) |
TSV |
| GSM8577747_Cond4_filtered_feature_bc_matrix.h5 |
6.6 Mb |
(ftp)(http) |
H5 |
| GSM8577747_Cond4_matrix.mtx.gz |
17.5 Mb |
(ftp)(http) |
MTX |
| GSM8577747_Cond4_scalefactors_json.json.gz |
171 b |
(ftp)(http) |
JSON |
| GSM8577747_Cond4_tissue_hires_image.png.gz |
4.6 Mb |
(ftp)(http) |
PNG |
| GSM8577747_Cond4_tissue_lowres_image.png.gz |
454.0 Kb |
(ftp)(http) |
PNG |
| GSM8577747_Cond4_tissue_positions_list.csv.gz |
67.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
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