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Sample GSM7146146 Query DataSets for GSM7146146
Status Public on Jan 16, 2024
Title Synovia of PsA patient ST2
Sample type SRA
 
Source name synovia
Organism Homo sapiens
Characteristics tissue: synovia
disease: psoriatic arthritis
Sex: female
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from synovial biopsies using the RNeasy kit and an RNase-free DNase set (Qiagen)
Library preparation, QC and 150PE Illumina sequencing services were provided by the external provider Novogene in accordance to the ENCODE guidelines for RNA-Seq (revised version Dec 2016). 30G of data were sequenced per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description PsA_ST2
Data processing The Salmon (v 1.5.2) index was generated using the GRCh38 human genome (GENCODE v38/Ensembl 104) with --type quasi -k 31
Transcript quantification was performed using Salmon (v 1.5.2) with --validateMapping, --useVBOpt and –seqBias
Transcript quantifications were converted to gene-level counts in R using the tximport (v 1.24.0)
DESeq2 (v 1.36.0) was used to correct for library size using “avgTxLength” (normalized_counts)
The “rlog” from DESeq22 (v 1.36.0) for regularised log transformation was used for count transformation (rlog_trnasformed_counts)
Assembly: GRCh38
Supplementary files format and content: Salmon quantification results in .tar format
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include normalized counts for each sample
Supplementary files format and content: tab-delimited text file include rlog transformed counts for each sample
 
Submission date Apr 04, 2023
Last update date Jan 16, 2024
Contact name Hashem Mohammadian
Organization name University of Erlangen-Nürnberg
Department Department of Medicine 3 - Rheumatology and Immunology
Street address Ulmenweg 18
City Erlangen
ZIP/Postal code 91054
Country Germany
 
Platform ID GPL24676
Series (2)
GSE228953 Molecular reframing of fibroblasts during resolution of arthritis [RNA]
GSE228982 Molecular reframing of fibroblasts during resolution of arthritis
Relations
BioSample SAMN34070598
SRA SRX19867689

Supplementary file Size Download File type/resource
GSM7146146_PsA_ST2_quant.tar.gz 2.9 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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