|
| Status |
Public on Jun 20, 2024 |
| Title |
C1_WM, snRNASeq |
| Sample type |
SRA |
| |
|
| Source name |
white matter
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: white matter
lesion: WM
age: 35
postmortem delay: 22
|
| Treatment protocol |
Fresh frozen tissue blocks
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FANS-sorted nuclei from postmortem human brain tissue
Guidelines from 10x Genomics (CG000183 Rev A)
Indexed adapters pooling single nucleus 3ʹ mRNA-sequencing with 1% PhIX
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
cellranger software version 6.1.2 with the reference refdata-gex-GRCh38-2020-A, using the –include-introns option recommended for single nucleus RNA sequencing data.
Empty droplets were removed using the R package DropletUtils, multiplets predicted using the hybrid method. We included only barcodes with at least 200 and fewer than 4000 genes and a mitochondrial read fraction of less than 1%
Scuttle’s pseudobulk aggregation was used to compute the meta cells for all cell types per sample. EdgeR’s likelihood ratio test accounting for the sex as an additional covariate was used to test for DE for WM vs lesion for each major cell type
Assembly: GRCh38 (refdata-gex-GRCh38-2020-A)
Supplementary files format and content: {sample_name}_raw_feature_bc_matrix.h5, unfiltered cellranger output
|
| |
|
| Submission date |
May 03, 2023 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Anne Hartebrodt |
| E-mail(s) |
anne.hartebrodt@fau.de
|
| Organization name |
University of Southern Denmark
|
| Street address |
Campusvej 55
|
| City |
Odense |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE231585 |
Gene expression profiling at single nucleus level of microdissected white matter tissue samples of patients with progressive multiple sclerosis and non-neurological disease controls |
| GSE231587 |
Progressive multiple sclerosis |
|
| Relations |
| BioSample |
SAMN34568991 |
| SRA |
SRX20209833 |
