Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ena-DATASET-ErasmusMC-hema-25-04-2021-16:56:25:942-1304 - samples

ABSTRACT: Sample libraries were prepped using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina) and aligned against the human genome (hg19) using STAR v2.5.4b2.

PROVIDER: EGAD00001007581 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

ena-DATASET-ErasmusMC-hema-01-05-2021-11:15:35:203-67 - samples

Project description:Sample libraries were prepped using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina) and aligned against the human genome (hg19) using STAR v2.5.4b2.

| EGAD00001007646 | EGA

ena-DATASET-ErasmusMC-hema-18-12-2020-23:58:17:929-91 - samples

Project description:RNA-seq was generated to investigate differences in gene expression between t(3;8) AML and other primary AMLs. Briefly, sample libraries were prepared using 500 ng of input RNA according to the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Amplified sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina

| EGAD00001006819 | EGA

RNA sequencing of invasive vulvar squamous cell carcinoma (VSCC)

Project description:We retrospectively identified cases of invasive vulvar squamous cell carcinoma. Formalin fixed, paraffin embedded tissues samples were retrieved. Sections were confirmed by H&E staining prior to analysis. Sections were processed by ribosomal RNA depletion and RNA-sequencing (KAPA RNA HyperPrep with RiboErase) (HMR). 23 patient samples had RNA of sufficient quality for analysis. HPV status was determined by a consensus of high-risk HPV RNA-ISH and HPV DNA PCR. Only samples that were positive in both assays were considered 'HPV-positive'.

2022-01-01 | GSE183454 | GEO

RNA-seq of longitudinal human blood and nose swab samples from a controlled human infection experiment with SARS-CoV-2 virus

Project description:Controlled human infection experiments enable longitudinal profiling of immune responses to a pathogen. 36 healthy volunteers aged 18-29 years, with no evidence of previous infection or vaccination, were inoculated with SARS-CoV-2 virus and quarantined for 14 days. Blood samples for RNA sequencing were collected into PAXgene tubes before virus challenge, 6 hours after challenge, daily thereafter for 14 days and on day 28. Mid-turbinate nose swabs for RNA sequencing were collected before virus challenge, and on days 1, 3, 5, 7, 10 and 14 after challenge, preserved in RNAprotect. 18 of 36 participants developed a replicative SARS-CoV-2 infection as evidenced by consecutive PCR-positive swabs for the virus. For every participant, blood RNA from selected days were extracted and depleted for genomic DNA and globin mRNA, before cDNA libraries were constructed using KAPA RNA HyperPrep with RiboErase kits. Libraries were sequenced on the Illumina NovaSeq 6000 platform using NovaSeq 6000 S4 Reagent Kits (200 cycles). Nose swab RNA samples were extracted and depleted for genomic DNA before cDNA libraries were constructed using KAPA mRNA HyperPrep Kits. Libraries were sequenced on the Illumina NextSeq platform the using the NextSeq 500/550 High Output Kit (75 cycles).

2024-04-08 | E-MTAB-12993 | biostudies-arrayexpress

CircRNA sequencing in peripheral blood mononuclear cells from Ankylosing Spondylitis patients and healthy controls

Project description:To identify the expression profiles of circRNAs in peripheral blood mononuclear cells (PBMCs) from Ankylosing Spondylitis (AS) patients and healthy controls, we used circRNA sequencing to detect circRNA in 3 samples of PBMCs from AS patients and 3 samples of PBMCs from healthy controls. In brief, total RNA was extracted and purified using Magen Hipure Total RNA Mini Kit (Magen, Guangzhou, China), followed by constructing RNA sequencing libraries with KAPA RNA HyperPrep Kit with RiboErase (Kapa Biosystems, Inc., MA, USA). After the construction of RNA sequencing libraries, Qubit 3.0 fluorometer (Invitrogen, CA, USA) and the Agilent 2100 bioanalyzer (Applied Biosystems, CA, USA) were used for quality control. Then, the PE150 mode of HiSeq X10 (Illumina Inc., CA, USA) was used for sequencing. Differentially expressed circRNAs were screened with criteria of fold-change>1.5 and p<0.05.

2022-01-05 | GSE178408 | GEO

192dfdfa-5885-4512-a4b9-b90100490cd8 - samples

Project description:For this project about non-muscle invasive bladder cancer (NMIBC), we analysed total RNA-seq data from 47 patients used for validation. Sequencing of total RNA was performed using KAPA RNA HyperPrep Kit with RiboErase HMR (Roche). RNA input was 100 to 500 ng. The dataset is composed of 94 fastq files.

| EGAD00001006967 | EGA

ena-DATASET-ErasmusMC-hema-25-04-2021-16:53:29:167-1303 - samples

Project description:The Genomic DNA Clean & Concentrator kit (ZYMO Research) was used to remove EDTA from the DNA samples. Sample libraries were prepared using 100 ng of input according to the KAPA HyperPlus Kit (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Exomes were captured using the SeqCap EZ MedExome (Roche Nimblegen) according to SeqCap EZ HyperCap Library v1.0 Guide (Roche) with the xGen Universal blockers Ã¢Â€Â“ TS Mix (Integrated DNA Technologies, Inc.). The amplified captured sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina) and aligned to the hg19 reference genome using the Burrows-Wheeler Aligner (BWA)3, v0.7.15-r1140.

| EGAD00001007580 | EGA

c7b48d06-6877-45d1-941a-593fef272a6b - samples

Project description:For this project about non-muscle invasive bladder cancer (NMIBC), we analysed total RNA-seq data from 535 patients. Sequencing of total RNA was performed using ScriptSeq-v2 RNA-Seq Library Preparation Kit (Illumina) and KAPA RNA HyperPrep Kit with RiboErase HMR (Roche). RNA input was 500 ng for both kits. The dataset is composed of 1,596 fastq files.

| EGAD00001006656 | EGA

Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in The White Adipose Tissues of Wild Type (WT) and Adipose-tissue-specific Ces1d knockout (Ces1d FKO) mice

Project description:The goal of this study is to analyze the white adipose tissue transcriptome profiling (RNA-seq) of the wild type and adipose-tissue-specific Ces1d knockout mice. Methods: White adipose tissue mRNA profiles of 14-week-HFD-fed wild-type (WT) and Ces1d adipose tissue knockout mice were collected. Total RNA quality was measured using Agilent RNA 6000 Pico kit (#5067-1513) by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA). The samples with RNA integrity number (RIN) greater than 7 were used for library preparation. Libraries were prepared with KAPA mRNA HyperPrep (KK8581, Roche) and KAPA UDI Adapter Kit 15μM (KK8727, Roche) following the manufacturer’s instructions. The pooled libraries (n = 10) were paired-end sequenced using 75-cycle High Output Kit v2.5 (#20024907, Illumina, Inc., USA) on Illumina NextSeq 550 System. We used ultrafast universal RNA-seq aligner STAR (v2.5.3a) to conduct the read alignment to mouse reference genome GRCm38. Gene read counts were calculated through setting the argument –quantMode to “GeneCounts” to let STAR count number of uniquely-mapped reads per gene from the GencodeM15 reference. Groups: WT, Sample 1-5; Ces1d FKO, Sample 6-10

2022-03-29 | GSE173893 | GEO

High-throughput sequencing identifies 25,303 circRNA targets, including 20,036 known circRNAs and 5,267 uncharacterized circRNAs, in gastric cancer tissues

Project description:Purpose: With the advent of human genome sequencing project, circRNAs attracted widespread attention in cancer research due to its stable ring structure. Our aim was to identify differentially expressed circRNAs in GC and explore their potential roles in GC diagnosis and treatment. Methods: Total RNA from tissues was isolated by Hipure Total RNA Mini Kit (Magen, Germany). Qubit 3.0 Fluorometer (Invitrogen, Carlsbad, California) was used for RNA concentration measurement while Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA) for RNA integrity estimation. A RIN value over 7.0 was considered eligible. RNA-seq library was prepared with approximately 2μg of total RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina® (Kapa Biosystems, Inc., Woburn, MA). Briefly, total RNA was incubated at 37 °C for 30 min with 10 units RNase R (Epicentre Technologies, Madison, USA) after removing ribosomal RNA. Next, the ribominus RNase R (+) RNAs was fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation were performed with the purified cDNA. Finally, the purified, adapter-ligated DNA was amplified. Each library was diluted to 10 nM and pooled equimolar prior to clustering. Paired-End (PE150) sequencing was performed on all samples. Results: A total of 25,303 circRNA targets, including 20,036 known circRNAs and 5,267 uncharacterized circRNAs, were detected and defined. Among them, there were 2,007 circRNAs with statistically significant differences in expression in GC tissues, in which fold changes>2.0 and P<0.05 were identified.

2019-06-16 | GSE131414 | 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