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| Status |
Public on Oct 16, 2024 |
| Title |
Dentate gyrus, Subject 4 |
| Sample type |
SRA |
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| Source name |
Dentate gyrus
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Dentate gyrus
Sex: Male
age: 21 years old
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh frozen tissue were OCT embedded and 10µm sections were cut with the cryostat
Spatial transcriptome sequencing libraries were prepared with the 10x Genomics Spatial Gene Expression slides and Reagent Kit according to the manufacturer's instructions
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Fresh frozen Spatial transcriptome sequencing
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| Data processing |
Raw sequencing data were processed using the 10x Genomics pipeline spaceranger to generate FASTQ files
Sequences were aligned to the GRCh38-2020-A genome to gene expression count using spaceranger's default settings
Gene expression level of Refseq coding genes were quantified using spaceranger's default settings
Space Ranger outputs of each sample were read into R (v. 4.1.0) in a customized structure using the Seurat R package (V4)
Spots with very high molecular counts were filtered out for two of the samples
The samples were then combined into a single Seurat object.
The data was normalized using the log-normalization procedure with NormalizeData function with Seurat.
Variable genes were identified using the FindVariableFeatures function (with the selection method set to vst and the number of features set to 2000) with Seurat.
The normalized dataset was next scaled using the ScaleData function with Seurat.
The top 50 principal components (PCs) were computed with the RunPCA function with Seurat.
The merged Seurat object was converted into a SingleCellExperiment (v.1.16.0) object for batch correction with the R package Harmony (v.0.1.0) and for spot clustering.
The first 15 PCs were used for downstream clustering using the BayesSpace (t-distributed error model) clustering algorithm (v. 1.4.1) with the SpatialCluster (nrep = 50 000) BayesSpace function.
Assembly: GRCh38
Supplementary files format and content: CombinedSeuratObject_HPC.rds: combined seurat object with all 4 subjects and containing BayesSpace (t-distributed error model) clustering data and tSNE (after batch correction with the R package Harmony) cell embeddings
Supplementary files format and content: A1_raw_feature_bc_matrix.h5: unfiltered feature-barcode matrix for library A1
Supplementary files format and content: B1_raw_feature_bc_matrix.h5: unfiltered feature-barcode matrix for library B1
Supplementary files format and content: C1_raw_feature_bc_matrix.h5: unfiltered feature-barcode matrix for library C1
Supplementary files format and content: D1_raw_feature_bc_matrix.h5: unfiltered feature-barcode matrix for library D1
Supplementary files format and content: spatial_A1.tar.gz: contains the spatial outputs of space ranger for library A1 (tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json and tissue_positions.csv)
Supplementary files format and content: spatial_B1.tar.gz: contains the spatial outputs of space ranger for library B1 (tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json and tissue_positions.csv)
Supplementary files format and content: spatial_C1.tar.gz: contains the spatial outputs of space ranger for library C1 (tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json and tissue_positions.csv)
Supplementary files format and content: spatial_D1.tar.gz: contains the spatial outputs of space ranger for library D1 (tissue_hires_image.png, tissue_lowres_image.png, aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json and tissue_positions.csv)
Library strategy: Spatial Transcriptomics
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| Submission date |
Nov 24, 2023 |
| Last update date |
Oct 16, 2024 |
| Contact name |
Naguib Mechawar |
| E-mail(s) |
naguib.mechawar@mcgill.ca
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| Organization name |
McGill University
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| Department |
Psychiatry
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| Lab |
McGill Group for Suicide Studies
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| Street address |
6875 Boulevard LaSalle
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H4H 1R3 |
| Country |
Canada |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE248545 |
Spatial transcriptomics analysis of adult hippocampal neurogenesis in the human brain |
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| Relations |
| BioSample |
SAMN38411807 |
| SRA |
SRX22635296 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7916584_D1_raw_feature_bc_matrix.h5 |
10.1 Mb |
(ftp)(http) |
H5 |
| GSM7916584_spatial_D1.tar.gz |
9.3 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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