|
| Status |
Public on Dec 02, 2023 |
| Title |
S163P46_SLE2 |
| Sample type |
SRA |
| |
|
| Source name |
whole blood
|
| Organism |
Homo sapiens |
| Characteristics |
sampleID: S163
pregnancyid: P46
tissue: whole blood
samplegroup: SLE
timepoint: 2
grouptime: SLE_2
das28: NA
lai(p): 0
medicationra: 0
medicationsle: 2
prednisolon use: 1
diseasestate: 0
disease state_and_medication_status: 1
library size: 15334901.801
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using PAX-gene blood RNA-kits (Qiagen)
RNA sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FASTQ files were created with bcl2fastq V2.20, quality controlled with fastqc (v0.11.9) and filtered and trimmed by fastp (v0.20.0). CollectRNASeqMetrics (v2.21.5)
Trimmed sequences were aligned to the genome reference using STAR (v2.7.3) and quality metrics were extracted with picard CollectRNASeqMetrics (v2.21.5).
Transcript counts were generated using quasi alignment (Salmon v1.3.0) to the GRCh38 transcriptome reference sequences and imported into the R statistical software and aggregated to gene expression counts using the tximport (v1.14.0)
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts (cpm) for 60218 ENSG numbers for 335 samples
|
| |
|
| Submission date |
Jun 21, 2023 |
| Last update date |
Dec 02, 2023 |
| Contact name |
Pål Sætrom |
| E-mail(s) |
pal.satrom@ntnu.no
|
| Phone |
+4798203874
|
| Organization name |
Norwegian University of Science and Technology, NTNU
|
| Department |
Clinical and Molecular Medicine
|
| Street address |
Erling Skjalgsons gate 1
|
| City |
Trondheim |
| ZIP/Postal code |
7491 |
| Country |
Norway |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE235508 |
Single-cell resolution of longitudinal blood transcriptome profiles in rheumatoid arthritis, systemic lupus erythematosus and healthy control pregnancies |
|
