|
| Status |
Public on Jul 26, 2021 |
| Title |
SjSHC11-CXCR5plus |
| Sample type |
SRA |
| |
|
| Source name |
HC_CXCR5+ Th cell
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: HC
tissue: Peripheral blood
cell type: CXCR5+ Th cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Venapuncture from patient or control. Fresh peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll density gradient centrifugation from Li-heparin blood. PBMCs were stained with fluorochrome-conjugated antibodies against CD3, CD4, CXCR5 and CCR9. CCR9+CXCR5- (CCR9+), CXCR5+CCR9- (CXCR5+) and CCR9-CXCR5- Th cells were sorted with Fluorescence-activated cell sorting (FACS) using BD FACSARIAIII and harvested into tubes with RPMI 1640 containing 10% FCS and 1% penicillin/streptomycin. Cells were lysed in RLTplus buffer (Qiagen) with 1% beta-mercaptoethanol. RNA was extracted using the AllPrep Universal Kit in QIACube (both Qiagen)
TruSeq RNA Library Prep Kit (Illumina) according to manufacturer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
FCH7V55BBXX-HKHUMmurEAAPRABPEI-218_L8
|
| Data processing |
Samples were sequenced on an Illumina HiSeq4000 generating approximately 20 million 150bp paired-ended reads
The sample qualities were assessed by FastQC.
HTSeq-count was used to generate read counts.
Variance-stabilizing transformation (VST) on the raw read counts was performed using R/Bioconductor package DESeq2 to obtain normalized read counts (NRC), which are log2 normalized.
Genome_build: The sequencing reads were aligned to human genome (GRCh38 build 79) using STAR aligner.
Supplementary_files_format_and_content: Matrix table with log2 normalized read counts for every gene and every sample (except for 2 HC CCR9+ samples that were excluded after quality contol using FastQC).
|
| |
|
| Submission date |
Apr 30, 2021 |
| Last update date |
Jul 26, 2021 |
| Contact name |
Anneline Hinrichs |
| Organization name |
University Medical Center Utrecht
|
| Department |
Rheumatology & Clinical Immunology
|
| Street address |
Postbus 85500
|
| City |
Utrecht |
| ZIP/Postal code |
3508 GA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE173635 |
Transcriptome analysis of CCR9+, CXCR5+ and CCR9-CXCR5- Th cells in primary Sjögren's syndrome (pSS) patients and healthy controls (HC) |
|
| Relations |
| BioSample |
SAMN18929311 |
| SRA |
SRX10721972 |
