|
| Status |
Public on Jan 21, 2020 |
| Title |
MS4_Sample_85 |
| Sample type |
SRA |
| |
|
| Source name |
MS4
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Multiple sclerosis
tissue: Brain
lesion type: Inactive (IL)
individual: MS4
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
miRNeasy Mini Kit (Qiagen).
TruSeq Stranded Total RNA library prep kit (Illumina).
Total RNA seq (deletion of ribosomal RNA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
processed data file: countMatrix.txt
|
| Data processing |
Sequenced reads were trimmed with trimmomatic: (TRIM:2:30:10 LEADING:20 TRAILING:20 SLIDING:4:20 TRAILING:20 MIN:17)
Mapping with STAR Aligner (version 2.5.3a).
Read counting with HTSeq-count (strict).
EdgeR was used to train generalized linear models to find differentially expressed genes while correcting for age, sex and sample distribution.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: countMatrix.txt contains read counts for every gene (row) and every sample (column).
Supplementary_files_format_and_content: Tab-separated text files with the results from EdgeR.
|
| |
|
| Submission date |
Oct 08, 2019 |
| Last update date |
Jan 21, 2020 |
| Contact name |
Tobias Frisch |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Southern Denmark
|
| Street address |
Campusvej 55
|
| City |
Odense M |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE138614 |
Next-generation sequencing study in multiple sclerosis white matter brain lesions |
|
| Relations |
| BioSample |
SAMN12995657 |
| SRA |
SRX6966541 |
