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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 09, 2024 |
| Title |
NBB17-005, Inferior frontal gyrus, Ctrl |
| Sample type |
SRA |
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| Source name |
IFG
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| Organism |
Homo sapiens |
| Characteristics |
tissue: IFG
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Extraction of nuclei was performed with the Nuclei PURE Prep Isolation Kit (Sigma-Aldrich, NUC201-1KT) as described in https://www.protocols.io/view/nuclei-isolation-from-human-cnssamples-using-nuc2-261genq1og47/v1
10X Genomics 3’ gene expression V3
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
FASTQ files were aligned with the human reference genome GRCh38 using 10X Genomics CellRanger v3.0.2. Velocyto (v.0.17.16) [32] was used to reintroduce unspliced mRNAs to the feature count matrix.
For .rds file: Quality control was carried out using Scater. Doublets were removed using scDblFinder. Data were normalised using Scran. Downstream analysis was carried out in Seurat: CCA was used to adjust for batch effects, PCA and UMAP were used for dimensional reduction. Clustering was performed as follows: A K-Nearest Neighbour (KNN) graph was built as basis for community detection using a Louvain algorithm.
Assembly: GRCh38
Supplementary files format and content: .fastq files: Index, R1 and R2 from L001 and L002 for each sample. .h5 files: Filtered and raw feature barcode matrix for each sample. .rds file: Seurat object containing all samples and annotations, .csv file: metadata corresponding to the Seurat object
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| Submission date |
Nov 04, 2024 |
| Last update date |
Nov 09, 2024 |
| Contact name |
Anna Williams |
| E-mail(s) |
anna.williams@ed.ac.uk
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| Organization name |
University of Edinburgh
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| Street address |
5 Little France Drive, Centre for Regenerative Medicine
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| City |
Edinburgh |
| State/province |
Edinburgh |
| ZIP/Postal code |
EH16 4UU |
| Country |
United Kingdom |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE281069 |
Mapping the glial transcriptome in Huntington’s disease using snRNAseq: Selective disruption of glial signatures across brain regions |
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| Relations |
| BioSample |
SAMN44575659 |
| SRA |
SRX26606122 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8610255_14931PJpool01-S_HD_27_NBB17-005_IFG_filtered_feature_bc_matrix.h5 |
7.8 Mb |
(ftp)(http) |
H5 |
| GSM8610255_14931PJpool01-S_HD_27_NBB17-005_IFG_raw_feature_bc_matrix.h5 |
134.2 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
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