Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ethnicity-specific transcriptomic variation in immune cells and correlation with disease activity in systemic lupus erythematosus

ABSTRACT: Participants were recruited from the California Lupus Epidemiology Study (CLUES). CLUES was approved by the Institutional Review Board of the University of California, San Francisco. Peripheral blood mononuclear cells were isolated from patient donors. Cells were isolated from peripheral blood utilizing magnetic beads (CD14+monocytes, B cells, CD4+T cells and NK cells) using EasySep protocol from STEM cell technologies on 120 patients. RNA and DNA were extracted using Qiagen column and quality was assessed on Agilent bioanalyzer. 1ng - 5ng of RNA was used with SmartSeqv2 protocol to get cDNA, followed by Illumina Nextera XT DNA library prep with input of 0.8ng cDNA and 15 cycles of PCR amplification. Both cDNA and DNA libraries qualities were controlled on Agilent bioanalyzer. Libraries were sequenced on HiSeq4000 PE150.

ORGANISM(S): Homo sapiens

PROVIDER: GSE164457 | GEO | 2021/03/04

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

scRNA-seq of vertebrobasilar aneurysm in polyarteritis nodosa patient

Project description:Endovascular biopsy and fluorescence activated cell sorting was used to enrich for viable endothelial cells (ECs) from a vertebrobasilar aneurysm and the femoral artery. scRNAseq was then performed on 24 aneurysmal endothelial cells and 23 patient-matched non-aneurysmal femoral artery endothelial cells. cDNA libraries were prepared using the Smart-seq2 protocol on a Fluidigm C1 system (Fluidigm, South San Francisco, California) and sequenced on a HiSeq2500 machine (Illumina, San Diego, California).

2021-07-01 | E-MTAB-10681 | biostudies-arrayexpress

Transcriptome sequencing Analysis of hLFSCs with and without mechanical stress

Project description:Purpose:The goals of this study are to MS (mechanical stress) how to change the cellular pathway of hLFSCs (human ligament flavum stem cells). Methods: Extract hLFSCs from the ligament flavum of patients.Treat the cells with and without (in control)MS.Total RNA was extracted from cells with Tripure Isolation Reagent.Subsequently, RNA was purified through rRNA depletion and then subjected to cDNA synthesis and RNA amplification. Next, random hexamer primer cDNA libraries were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and sequenced on Illumina Hiseq 4000 sequencing platform (Illumina, San Diego, California, USA) following the manufacturer’s instructions for paired-end 150 bp reads (Lifegenes, Shanghai, China).

2021-10-13 | GSE185614 | GEO

Transcriptome analysis of total RNA in human osteosarcoma cell line U2OS before and after inhibition of zinc finger protein ZNF768

Project description:Inhibition of ZNF768 function was achieved by conditional over expression expression of the C-terminal zinc finger of ZNF768 for 12h. For preparation of total RNA cells were resuspended in TRIzol reagent (Life Technologies) at 0.9Mio/ml and snap-frozen. After thawing RNA was extracted from 0.4ml of TriZol lysate using the direct-zol RNA Miniprep (Zymo Research, Irvine CA, USA) as described in the manufacturer’s protocol. RNA was assessed for purity by UV-vis spectrometry (Nanodrop) and for integrity by Bioanalyzer (Agilent Bioanalyzer 2100, Agilent, Santa Clara USA)). RNA was of high purity (abs. 260/280 >1.9, abs 269/239>2.1) and integrity (Bioanalyzer RIN>9 ) and thus used for further processing. For production of RNA-seq libraries total RNA was DNAse treated (dsDNAse, Fermentas) and 100 ng of this RNA was processed with a strand-specific protocol (RNA-seq complete kit, NuGEN, San Carlos, USA). In brief the RNA was reverse transcribed to cDNA with a reduced set of hexamer primers, avoiding excessive representation of rRNA in the cDNA. Second strand cDNA synthesis was done in presence of dUTP. After ultrasonic fragmentation of the cDNA and end repair, Illumina-compatible adapter were ligated. Adapters contained uracil in one strand, allowing complete digestion of the second-strand derived DNA. After strand selection the libraries were amplified, assessed for correct insert size on the Agilent Bioanalyser and diluted to 10nM. Barcoded libraries were mixed in equimolar amounts and sequenced on an Illumina HiSeq1500 in single-read mode with a read length of 100 b.

2018-10-29 | GSE111881 | GEO

miRNA and mRNA Signatures in Human Acute Kidney Injury Tissue [mRNA, minimal change disease]

Project description:Acute kidney injury (AKI) is an important contributor to the development of chronic kidney disease (CKD). We performed miRNA and mRNA sequencing on biobanked human kidney tissues obtained in the routine clinical care of patients with the diagnoses of AKI and minimal change disease (MCD), in addition to nephrectomized (Ref) tissue from individuals without known kidney disease. From all renal biopsy samples, 2 cryosections (10 μM) including the entire cross-section of the tissue were placed directly into PicoPure RNA extraction buffer. RNA was isolated using the PicoPure isolation kit. Total RNA was evaluated for quantity and quality using an Agilent Bioanalyzer. Approximately 10 ng of total RNA were used for each sample’s library preparation. Ribosomal RNA was removed using RiboGone – Mammalian Kit protocol. After rRNA depletion, double-stranded cDNA was synthesized and amplified using the SMARTer Universal Low Input RNA Kit protocol. The cDNA was sheared by Covaris, and the library was prepared and barcoded following the Ion Plus Fragment Library Kit protocol. Each resulting barcoded library was quantified and quality assessed by Agilent Bioanalyzer. Multiple libraries were pooled in equal molarity. Finally, 8 μL of 100 pM pooled libraries were loaded into lanes of an Illumina HiSeq 4000. At least 30M reads per library were generated.

2024-07-11 | GSE246204 | GEO

RNASeq of Candida-stimulated CD3+ T-cells from individuals with CARD9 mutations and normal controls

Project description:CD3+ T cells were enriched using the EasySep human T cell isolation kit (Stem cell technology). T cells from normal controls or patients with CARD9 mutations were co-cultured with monocytes of one normal control in the presence of heat killed candida. After 3 days, T cell were enriched again to remove the monocytes and total RNA was extracted from the T cells for the RNA-sequencing (RNASeq) evaluation. Targeted RNA sequencing library preparation was carried out using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Life Technologies), which profiles more than 20,000 human genes; each amplicon (~150 bp) represents a unique targeted gene (one transcript per gene). For library preparation, each sample was run in duplicate, and a cDNA library was generated from a minimum of 10 ng of total RNA. The cDNA was barcoded and amplified with Ion AmpliSeq technology, and the amplified cDNA Libraries were evaluated for quality and quantified with Agilent Bioanalyzer high-sensitivity chip. Libraries were then diluted to 100 pM and pooled equally, with 4 individual samples per pool. Pooled libraries were amplified and enriched with the Ion Chef System (Life Technologies). Templated libraries were then sequenced on an Ion Torrent Proton sequencing system (Life Technologies) with Ion PI HiQ kit and chip version 3. We performed gene-level differential expression analysis of targeted RNASeq data using R (v.3.5.3) and the Bioconductor packages DESeq2 (v.1.22.2).

2021-08-12 | GSE181718 | GEO

Postnatal loss of Arx transcriptional activity in parvalbumin interneurons induces epilepsy-like network abnormalities

Project description:We report the use to RNA-sequencing to understand the role of postnatal Arx in the regulation of PV interneuron function. Total RNA extracted from control and Arx CKO male mice cells were submitted to the Next-Generation Sequencing Core of the University of Pennsylvania for cDNA amplification, library preparation, and sequencing using the Ovation RNA-seq v2 and Rapid DR Multiplexing kits (NuGEN). Whole mRNAseq libraries were prepared from 9 mice (5 control and 4 Arx CKO mice) using the SMARTer Ultra Low RNA Kit for Illumina Sequencing (Clontech, Cat#634936) according to manufacturer’s instructions. Standard methods to assess sample quality (Agilent Bioanalyzer, Kappa Biosystems Library Quantification kit, Qubit® Fluorometer) and measure cDNA concentration were used. A total of 1ng of amplified cDNA for each sample was used as input to build the sequencing libraries. Whole mRNAseq libraries from control and Arx CKO mice were quantified using Agilent Bioanalyzer DNA 7500 chips. Libraries were sequenced on the Illumina HiSeq 4000 2 × 100 (Illumina, San Diego, CA, USA) to generate 150bp paired end reads, yielding approximately 20-40 million reads per sample (~80 million reads per lane).

2020-09-09 | GSE157689 | GEO

RNA sequencing of bone marrow macrophages from non-Hodgkin lymphoma Raji cell engrafted mice

Project description:Purpose: The study aimed to characterize the molecular phenotype of bone marrow macrophages in NHL with RNA sequencing analysis. Methods:RNA of sorted femur macrophages (CD11b+F4/80+) were extracted with an RNA extraction kit (Qiagen). The samples were submitted to Novogene Inc. for library preparation and subsequent RNA sequencing. RNA was used for cDNA library construction using an NEBNext® Ultra RNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s protocol. The resulting 250-350 bp insert libraries were quantified using a Qubit 2.0 fluorometer (Thermo Fisher Scientific) and quantitative PCR. Size distribution was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Qualified libraries were sequenced on an Illumina HiSeq 4000 Platform (Illumina) using a paired-end 150 run (2×150 bases). Reads containing adapter or poly-N and those of low quality were trimmed, after which gene counts were obtained though mapping the clean reads to reference genome mm10 using STAR 2.5.3a.

2021-12-12 | GSE190598 | GEO

Integrated Analysis of Population Genomics, Transcriptomics and Virulence Provides Novel Insights into Streptococcus pyogenes Pathogenesis [442 strains]

Project description:Purpose: We used GAS as a model bacterial pathogen to investigate the complex relationship between genome, transcriptome, and virulence in a large population of type emm28 strains recovered from humans over 26 years in geographically diverse locations. Methods: We chose a subset of isolates from the sequenced population of 2,101 emm28 strains that would approximately span the genetic variation present in the entire population. 442 emm28 strains grown as singleton cultures and harvested at one time point (early-stationary phase), and libraries were prepared using RNAtag-seq. Quality of the total RNA, rRNA-depleted RNA, and cDNA libraries was evaluated with RNA Nano, RNA Pico, and DNA high-sensitivity kits (Agilent Technologies), respectively, using an Agilent 2100 Bioanalyzer. For each sample, the cDNA library concentration was measured fluorometrically with Qubit™ dsDNA HS assay kits (Invitrogen). The cDNA libraries were diluted, pooled, and sequenced with an Illumina NextSeq 500 instrument.

2018-12-31 | GSE113055 | GEO

EWS-Fli and LNC regulated genes in comparison to GFP samples

Project description:RNA from A673 cells with shRNA-mediated knockdown of GFP (4 libraries), EWS-FLI1 (4 libraries), or lnc277 (7 libraries) was isolated with TRIzol (Invitrogen). Each sample was DNase treated and further purified on an RNeasy Mini column (Qiagen) before quality analysis on an Agilent 2100 Bioanalyzer. For each sample, 100-150ng of RNA was synthesized into cDNA, sheared on a Covaris ultrasonicator, and amplified using the NuGen Encore Complete kit (NuGen) to produce strand-specific and rRNA-depleted libraries. Samples were multiplexed (4/lane) for 2x100bp paired-end sequencing on an Illumina HiSeq 2000

2014-11-01 | GSE60949 | GEO

Microarray analysis of lung SPC/GFP+ EpCAM+ cells

Project description:We extracted RNA of sorted lung SPC/GFP+ EpCAM+ cells and performed microarray analyses. Total RNA was extracted from sorted Ep-CAMhigh/GFPhigh cells using TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocol. The RNA integrity was examined on an Agilent 2100 BioAnalyzer (Agilent Technologies, Santa Clara, CA). Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using the GeneChip WT PLUS Reagent Kit User Manual (Affymetrix/Thermo Fisher Scientific). Fragmented and labeled ss-cDNA were hybridized on a GeneChip Clariom S Array (Affymetrix/Thermo Fisher Scientific) (n =3/group). We used microarrays to detail the global gene expression of SPC/GFP+ EpCAM+ cells from the control mice(G29-5_(Clariom_S_Mouse)) and the 3 months smoke mice(G29-6_(Clariom_S_Mouse)), and identified distinct classes of up-regulated genes during this process.

2019-04-26 | GSE130331 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data