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Sample GSM7504193 Query DataSets for GSM7504193
Status Public on Dec 02, 2023
Title S108P31_SNRA0
Sample type SRA
 
Source name whole blood
Organism Homo sapiens
Characteristics sampleID: S108
pregnancyid: P31
tissue: whole blood
samplegroup: SNRA
timepoint: 0
grouptime: SNRA_0
das28: 1.79
lai(p): NA
medicationra: 0
medicationsle: NA
prednisolon use: 0
diseasestate: 0
disease state_and_medication_status: 0
library size: 5777009.58
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

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

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