Upper cortical layer-driven network impairment in schizophrenia - 10x genomics v3 snRNA-seq and Visium spatial transcriptomics datasets
This dataset contains 10x Genomics v3 3’ single nuclei RNA sequencing (24 human schizophrenia and control samples) and 10x Genomics Visium spatial transcriptomics (14 human schizophrenia and control samples) datasets. Files are in .bam format, output of the cellranger v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/3.1/using/count) for snRNA-seq and spaceranger v1.1.0 (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/1.1/using/count) for Visium samples. Reads were mapped against Release 97 of human genome from Ensembl (http://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz http://ftp.ensembl.org/pub/release-97/gtf/homo_sapiens/Homo_sapiens.GRCh38.97.gtf.gz). More details on sample processing are available in the biorXiv pre-print (https://doi.org/10.1101/2020.11.17.386458) and upcoming publication in Science Advances. BAM files can be converted to fastq files using bamtofastq tool (https://support.10xgenomics.com/docs/bamtofastq) with downstream remapping using tools and genomes of choice.
- 38 samples
- DAC: EGAC00001002810
- Technologies: Illumina NovaSeq 6000, NextSeq 500
- None DUO:0000001 (version: 2021-02-23)data use permissionA data item that is used to indicate consent permissions for datasets and/or materials, and relates to the purposes for which datasets and/or material might be removed, stored or used.
- PUB DUO:0000019 (version: 2021-02-23)publication requiredThis data use modifier indicates that requestor agrees to make results of studies using the data available to the larger scientific community.
- NCU DUO:0000046 (version: 2021-02-23)non-commercial use onlyThis data use modifier indicates that use of the data is limited to not-for-profit use.
Data access and use policy for schizophrenia and control cases sequencing data
Data distributed in this repository can be downloaded upon getting permission from DAC Data can be re-analyzed Data can be used in other scientific publications or for commercial use, but original study should be referenced (bioRxiv pre-print https://doi.org/10.1101/2020.11.17.386458; and upcoming publication that will be mentioned on bioRxiv pre-print when paper gets published) Contact DAC for DAA
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| EGAS00001006495 | Other |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
| ID | File Type | Size | Located in | |
|---|---|---|---|---|
| EGAF00006772270 | bam | 40.1 GB | ||
| EGAF00006772271 | bam | 39.0 GB | ||
| EGAF00006772272 | bam | 40.6 GB | ||
| EGAF00006772273 | bam | 39.4 GB | ||
| EGAF00006772274 | bam | 43.5 GB | ||
| EGAF00006772275 | bam | 47.2 GB | ||
| EGAF00006772276 | bam | 37.0 GB | ||
| EGAF00006772277 | bam | 38.7 GB | ||
| EGAF00006772278 | bam | 47.3 GB | ||
| EGAF00006772279 | bam | 44.2 GB | ||
| EGAF00006772280 | bam | 43.2 GB | ||
| EGAF00006772281 | bam | 34.0 GB | ||
| EGAF00006772282 | bam | 42.1 GB | ||
| EGAF00006772283 | bam | 33.1 GB | ||
| EGAF00006772284 | bam | 43.5 GB | ||
| EGAF00006772285 | bam | 49.9 GB | ||
| EGAF00006772286 | bam | 26.5 GB | ||
| EGAF00006772287 | bam | 50.3 GB | ||
| EGAF00006772288 | bam | 42.6 GB | ||
| EGAF00006772289 | bam | 35.8 GB | ||
| EGAF00006772290 | bam | 35.5 GB | ||
| EGAF00006772291 | bam | 63.7 GB | ||
| EGAF00006772292 | bam | 46.4 GB | ||
| EGAF00006772293 | bam | 35.3 GB | ||
| EGAF00006772294 | bam | 6.6 GB | ||
| EGAF00006772295 | bam | 1.8 GB | ||
| EGAF00006772296 | bam | 6.9 GB | ||
| EGAF00006772297 | bam | 3.2 GB | ||
| EGAF00006772298 | bam | 6.1 GB | ||
| EGAF00006772299 | bam | 4.5 GB | ||
| EGAF00006772300 | bam | 14.6 GB | ||
| EGAF00006772301 | bam | 3.2 GB | ||
| EGAF00006772302 | bam | 7.2 GB | ||
| EGAF00006772303 | bam | 18.4 GB | ||
| EGAF00006772304 | bam | 24.6 GB | ||
| EGAF00006772305 | bam | 15.0 GB | ||
| EGAF00006772306 | bam | 5.5 GB | ||
| EGAF00006772307 | bam | 3.2 GB | ||
| 38 Files (1.1 TB) | ||||