|
| Status |
Public on Aug 08, 2023 |
| Title |
MS Responder 5 Baseline |
| Sample type |
SRA |
| |
|
| Source name |
Cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Cells
cell line: Primary
cell type: Peripheral blood mononuclear cells
treatment: None
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from PBMCs was extracted using the Maxwell 16 LEV simply RNA Cells kit (Promega Biotech Ibérica) on the Maxwell 16 instrument, according to the manufacturer’s instructions.
Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina’s recommendations. Briefly, poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA went through an end repair process, addition of a single “A” base to the 3’ end and ligation to the adapters. Finally, the products were purified and enriched with PCR to create the indexed final double stranded DNA library. The quality and quantity of the libraries were analysed in tapeStation 4200, using the High Sensitivity assay (Agilent Technologies
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control of the raw sequencing reads was performed with FastQC v.0.11.9.
Adapter sequences were trimmed with cutadapt v2.10.
Trimmed reads were quantified with Salmon v.1.3.0 and summarized to the gene level with tximeta v.1.6.3
Assembly: Salmon was used in selective alignment mode with the entire human genome as a decoy sequence.
Supplementary files format and content: tab-delimited excel file includes raw counts for each sample
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Alicia Sanchez |
| E-mail(s) |
alicia.sanchez@idiphim.org
|
| Organization name |
Instituto de Investigación Sanitaria Puerta de Hierro-Segovia de Arana
|
| Street address |
Joaquín Rodrigo, 2 Majadahonda
|
| City |
Madrid |
| ZIP/Postal code |
28222 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE235357 |
Transcriptomic profile of multiple sclerosis patients treated with dimethyl fumarate and their age and sex-matched healthy controls |
|
| Relations |
| BioSample |
SAMN35810098 |
| SRA |
SRX20729379 |
