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| Status |
Public on Dec 05, 2022 |
| Title |
WM_Lesion, CD4, 02 |
| Sample type |
SRA |
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| Source name |
WM_Lesion
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| Organism |
Homo sapiens |
| Characteristics |
tissue: WM_Lesion
cell number: 14616
tcell: CD4
lesion type: 3.3
patient: 02
age: 66
Sex: F
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| Treatment protocol |
Brain T cells were isolated from post-mortem brain tissue using enzymatic dissociation, followed by density gradient centrifugation and fluorescence-activated cell sorting using live/dead, CD3, CD4, CD8, CD69, and CD103 staining.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted cells were lysed in buffer RLT (QIAGEN) plus 1% β-mercaptoethanol and stored at -80°C until further processing. Total RNA was isolated with the RNeasy micro kit (QIAGEN) according to the manufacturers’ instructions.
PolyA-enrichment and NebNEXT low input library prep kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
104315-001-011
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| Data processing |
Adapter sequences were trimmed using Trimmomatic (version 0.39).
Trimmed reads were mapped to the human GRCh38 genome using HISAT2 (version 2.2.1) on default settings
Feature counts of reads mapped to genes were determined using HTSeq (version 1.99.2) with the ‘Homo_sapiens.CRCh38.105.gtf’ file (options: -m union -f bam -r name -s no -a 10 -t exon -i gene_id)
Resulting counts of both datasets were analyzed separately using R (version 4.2.0) and Bioconductor (version 3.15)
Assembly: GRCh38
Supplementary files format and content: tab-delimited .txt file containing raw, unnormalised counts for each sample
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| Submission date |
Oct 18, 2022 |
| Last update date |
Dec 05, 2022 |
| Contact name |
Jeen Engelenburg |
| E-mail(s) |
[email protected]
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| Organization name |
Netherlands Institute for Neuroscience
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| Lab |
Neuroimmunology lab
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| Street address |
Meibergdreef 47
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| City |
Amsterdam |
| ZIP/Postal code |
1105BA |
| Country |
Netherlands |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE216028 |
Transcriptional profiling of brain CD4+ and CD8+ TRM cells reveals dominant presence in white and grey matter in Multiple Sclerosis (MS) |
| GSE216030 |
Transcriptional profiling of brain CD4+ and CD8+ TRM cells reveals dominant presence in white and grey matter in Multiple Sclerosis |
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| Relations |
| BioSample |
SAMN31352980 |
| SRA |
SRX17937631 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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